@misc{9867, abstract = {In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental game instructions}}, doi = {10.1371/journal.pone.0163867.s008}, year = {2016}, } @misc{9868, abstract = {The raw data file containing the experimental decisions of all our study subjects.}, author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred}, publisher = {Public Library of Science}, title = {{Experimental data}}, doi = {10.1371/journal.pone.0163867.s009}, year = {2016}, } @misc{9869, abstract = {A lower bound on the error of a positional estimator with limited positional information is derived.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Error bound on an estimator of position}}, doi = {10.1371/journal.pone.0163628.s001}, year = {2016}, } @article{987, abstract = {In contrast to bulk FeSe, which exhibits nematic order and low temperature superconductivity, highly doped FeSe reverses the situation, having high temperature superconductivity appearing alongside a suppression of nematic order. To investigate this phenomenon, we study a minimal electronic model of FeSe, with interactions that enhance nematic fluctuations. This model is sign problem free, and is simulated using determinant quantum Monte Carlo (DQMC). We developed a DQMC algorithm with parallel tempering, which proves to be an efficient source of global updates and allows us to access the region of strong interactions. Over a wide range of intermediate couplings, we observe superconductivity with an extended s-wave order parameter, along with enhanced, but short-ranged, q=(0,0) ferro-orbital (nematic) order. These results are consistent with approximate weak-coupling treatments that predict that nematic fluctuations lead to superconducting pairing. Surprisingly, in the parameter range under study, we do not observe nematic long-range order. Instead, at stronger coupling an unusual insulating phase with q=(π,π) antiferro-orbital order appears, which is missed by weak-coupling approximations.}, author = {Dumitrescu, Philipp T and Maksym Serbyn and Scalettar, Richard T and Vishwanath, Ashvin K}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {15}, publisher = {American Physical Society}, title = {{Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study}}, doi = {10.1103/PhysRevB.94.155127}, volume = {94}, year = {2016}, } @misc{9870, abstract = {The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Computation of positional information in an Ising model}}, doi = {10.1371/journal.pone.0163628.s002}, year = {2016}, } @misc{9871, abstract = {The positional information in a discrete morphogen field with Gaussian noise is computed.}, author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Computation of positional information in a discrete morphogen field}}, doi = {10.1371/journal.pone.0163628.s003}, year = {2016}, } @misc{9873, author = {Boehm, Alex and Arnoldini, Markus and Bergmiller, Tobias and Röösli, Thomas and Bigosch, Colette and Ackermann, Martin}, publisher = {Public Library of Science}, title = {{Quantification of the growth rate reduction as a consequence of age-specific mortality}}, doi = {10.1371/journal.pgen.1005974.s015}, year = {2016}, } @inproceedings{1082, abstract = {In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y.}, author = {Chalk, Matthew J and Marre, Olivier and Tkacik, Gasper}, location = {Barcelona, Spain}, pages = {1965--1973}, publisher = {Neural Information Processing Systems}, title = {{Relevant sparse codes with variational information bottleneck}}, volume = {29}, year = {2016}, } @article{1083, abstract = { Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. }, author = {Booker, Sam and Althof, Daniel and Gross, Anna and Loreth, Desiree and Müller, Johanna and Unger, Andreas and Fakler, Bernd and Varro, Andrea and Watanabe, Masahiko and Gassmann, Martin and Bettler, Bernhard and Shigemoto, Ryuichi and Vida, Imre and Kulik, Ákos}, journal = {Cerebral Cortex}, number = {3}, pages = {2318 -- 2334}, publisher = {Oxford University Press}, title = {{KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons}}, doi = {10.1093/cercor/bhw090}, volume = {27}, year = {2016}, } @article{1088, abstract = {Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.}, author = {Uhler, Caroline and Shivashankar, G V}, journal = {BioArchitecture}, number = {4}, pages = {76 -- 84}, publisher = {Taylor & Francis}, title = {{Geometric control and modeling of genome reprogramming}}, doi = {10.1080/19490992.2016.1201620}, volume = {6}, year = {2016}, } @inproceedings{1090, abstract = { While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, location = {Krakow; Poland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Nested weighted limit-average automata of bounded width}}, doi = {10.4230/LIPIcs.MFCS.2016.24}, volume = {58}, year = {2016}, } @inproceedings{1093, abstract = {We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. }, author = {Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Petrov, Tatjana}, location = {Quebec City; Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Linear distances between Markov chains}}, doi = {10.4230/LIPIcs.CONCUR.2016.20}, volume = {59}, year = {2016}, } @inbook{1094, abstract = {Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face.}, author = {Harada, Harumi and Shigemoto, Ryuichi}, booktitle = {High-Resolution Imaging of Cellular Proteins}, issn = {1611-3349}, pages = {203 -- 216}, publisher = {Springer}, title = {{Immunogold protein localization on grid-glued freeze-fracture replicas}}, doi = {10.1007/978-1-4939-6352-2_12}, volume = {1474}, year = {2016}, } @inproceedings{1095, abstract = { The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. }, author = {Haas, Andreas and Henzinger, Thomas A and Holzer, Andreas and Kirsch, Christoph and Lippautz, Michael and Payer, Hannes and Sezgin, Ali and Sokolova, Ana and Veith, Helmut}, booktitle = {Leibniz International Proceedings in Informatics}, location = {Quebec City; Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Local linearizability for concurrent container-type data structures}}, doi = {10.4230/LIPIcs.CONCUR.2016.6}, volume = {59}, year = {2016}, } @article{1096, author = {Schwayer, Cornelia and Sikora, Mateusz K and Slovakova, Jana and Kardos, Roland and Heisenberg, Carl-Philipp J}, journal = {Developmental Cell}, number = {6}, pages = {493 -- 506}, publisher = {Cell Press}, title = {{Actin rings of power}}, doi = {10.1016/j.devcel.2016.05.024}, volume = {37}, year = {2016}, } @inproceedings{1097, abstract = {We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics.}, author = {Du, Tao and Schulz, Adriana and Zhu, Bo and Bickel, Bernd and Matusik, Wojciech}, location = {Macao, China}, number = {6}, publisher = {ACM}, title = {{Computational multicopter design}}, doi = {10.1145/2980179.2982427}, volume = {35}, year = {2016}, } @inproceedings{1098, abstract = {Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.}, author = {Pentina, Anastasia and Urner, Ruth}, location = {Barcelona, Spain}, pages = {3619--3627}, publisher = {Neural Information Processing Systems}, title = {{Lifelong learning with weighted majority votes}}, volume = {29}, year = {2016}, } @inproceedings{1099, abstract = {We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies.}, author = {Malomo, Luigi and Pietroni, Nico and Bickel, Bernd and Cignoni, Paolo}, location = {Macao, China}, number = {6}, publisher = {ACM}, title = {{FlexMolds: Automatic design of flexible shells for molding}}, doi = {10.1145/2980179.2982397}, volume = {35}, year = {2016}, } @article{1100, abstract = {During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.}, author = {Sako, Keisuke and Pradhan, Saurabh and Barone, Vanessa and Inglés Prieto, Álvaro and Mueller, Patrick and Ruprecht, Verena and Capek, Daniel and Galande, Sanjeev and Janovjak, Harald L and Heisenberg, Carl-Philipp J}, journal = {Cell Reports}, number = {3}, pages = {866 -- 877}, publisher = {Cell Press}, title = {{Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation}}, doi = {10.1016/j.celrep.2016.06.036}, volume = {16}, year = {2016}, } @article{1101, abstract = {Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of >300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.}, author = {Mitchell, Joshua and Whitfield, Jason and Zhang, William and Henneberger, Christian and Janovjak, Harald L and O'Mara, Megan and Jackson, Colin}, journal = {ACS SENSORS}, number = {11}, pages = {1286 -- 1290}, publisher = {American Chemical Society}, title = {{Rangefinder: A semisynthetic FRET sensor design algorithm}}, doi = {10.1021/acssensors.6b00576}, volume = {1}, year = {2016}, }