@inproceedings{10749,
  abstract     = {Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures.},
  author       = {Polshyn, Hryhoriy and Budakian, Raffi and Gu, Genda},
  booktitle    = {APS March Meeting 2013},
  issn         = {0003-0503},
  location     = {Baltimore, MD, United States},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Cantilever micro-susceptometry of mesoscopic Bi2212 samples}},
  volume       = {58},
  year         = {2013},
}

@article{10895,
  abstract     = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. },
  author       = {Vanneste, Steffen and Friml, Jiří},
  issn         = {2223-7747},
  journal      = {Plants},
  keywords     = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics},
  number       = {4},
  pages        = {650--675},
  publisher    = {MDPI},
  title        = {{Calcium: The missing link in auxin action}},
  doi          = {10.3390/plants2040650},
  volume       = {2},
  year         = {2013},
}

@inproceedings{10897,
  abstract     = {Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.},
  author       = {Edelsbrunner, Herbert},
  booktitle    = {Graph-Based Representations in Pattern Recognition},
  isbn         = {9783642382208},
  issn         = {1611-3349},
  location     = {Vienna, Austria},
  pages        = {182--183},
  publisher    = {Springer Nature},
  title        = {{Persistent homology in image processing}},
  doi          = {10.1007/978-3-642-38221-5_19},
  volume       = {7877},
  year         = {2013},
}

@inproceedings{10898,
  abstract     = {A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.},
  author       = {Haas, Andreas and Lippautz, Michael and Henzinger, Thomas A and Payer, Hannes and Sokolova, Ana and Kirsch, Christoph M. and Sezgin, Ali},
  booktitle    = {Proceedings of the ACM International Conference on Computing Frontiers - CF '13},
  isbn         = {978-145032053-5},
  location     = {Ischia, Italy},
  number       = {5},
  publisher    = {ACM},
  title        = {{Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation}},
  doi          = {10.1145/2482767.2482789},
  year         = {2013},
}

@inbook{10899,
  author       = {Barton, Nicholas H},
  booktitle    = {Encyclopedia of Biodiversity},
  isbn         = {978-0-12-384720-1},
  keywords     = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation},
  pages        = {508--515},
  publisher    = {Elsevier},
  title        = {{Differentiation}},
  doi          = {10.1016/b978-0-12-384719-5.00031-9},
  year         = {2013},
}

@inbook{10900,
  abstract     = {Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.},
  author       = {Weber, Michele and Sixt, Michael K},
  booktitle    = {Chemokines},
  editor       = {Cardona, Astrid and Ubogu, Eroboghene},
  isbn         = {9781627034258},
  issn         = {1940-6029},
  pages        = {215--226},
  publisher    = {Humana Press},
  title        = {{Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations}},
  doi          = {10.1007/978-1-62703-426-5_14},
  volume       = {1013},
  year         = {2013},
}

@inproceedings{10902,
  abstract     = {We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language.},
  author       = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Rubin, Sasha},
  booktitle    = {7th International Conference on Language and Automata Theory and Applications},
  isbn         = {9783642370632},
  issn         = {1611-3349},
  location     = {Bilbao, Spain},
  pages        = {214--225},
  publisher    = {Springer Nature},
  title        = {{How to travel between languages}},
  doi          = {10.1007/978-3-642-37064-9_20},
  volume       = {7810},
  year         = {2013},
}

@article{11083,
  abstract     = {Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.},
  author       = {Franks, Tobias M. and HETZER, Martin W},
  issn         = {0962-8924},
  journal      = {Trends in Cell Biology},
  keywords     = {Cell Biology},
  number       = {3},
  pages        = {112--117},
  publisher    = {Elsevier},
  title        = {{The role of Nup98 in transcription regulation in healthy and diseased cells}},
  doi          = {10.1016/j.tcb.2012.10.013},
  volume       = {23},
  year         = {2013},
}

@article{11084,
  abstract     = {Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing.},
  author       = {Toyama, Brandon H. and HETZER, Martin W},
  issn         = {1471-0072},
  journal      = {Nature Reviews Molecular Cell Biology},
  keywords     = {Cell Biology, Molecular Biology},
  pages        = {55--61},
  publisher    = {Springer Nature},
  title        = {{Protein homeostasis: Live long, won't prosper}},
  doi          = {10.1038/nrm3496},
  volume       = {14},
  year         = {2013},
}

@article{11085,
  abstract     = {During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy.},
  author       = {Hatch, Emily M. and Fischer, Andrew H. and Deerinck, Thomas J. and HETZER, Martin W},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {1},
  pages        = {47--60},
  publisher    = {Elsevier},
  title        = {{Catastrophic nuclear envelope collapse in cancer cell micronuclei}},
  doi          = {10.1016/j.cell.2013.06.007},
  volume       = {154},
  year         = {2013},
}

@article{11086,
  abstract     = {Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.},
  author       = {Liang, Yun and Franks, Tobias M. and Marchetto, Maria C. and Gage, Fred H. and HETZER, Martin W},
  issn         = {1553-7404},
  journal      = {PLoS Genetics},
  keywords     = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics},
  number       = {2},
  publisher    = {Public Library of Science},
  title        = {{Dynamic association of NUP98 with the human genome}},
  doi          = {10.1371/journal.pgen.1003308},
  volume       = {9},
  year         = {2013},
}

@article{11087,
  abstract     = {Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.},
  author       = {Toyama, Brandon H. and Savas, Jeffrey N. and Park, Sung Kyu and Harris, Michael S. and Ingolia, Nicholas T. and Yates, John R. and HETZER, Martin W},
  issn         = {0092-8674},
  journal      = {Cell},
  keywords     = {General Biochemistry, Genetics and Molecular Biology},
  number       = {5},
  pages        = {971--982},
  publisher    = {Elsevier},
  title        = {{Identification of long-lived proteins reveals exceptional stability of essential cellular structures}},
  doi          = {10.1016/j.cell.2013.07.037},
  volume       = {154},
  year         = {2013},
}

@article{11088,
  abstract     = {The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM.},
  author       = {Regner, Benjamin M. and Vučinić, Dejan and Domnisoru, Cristina and Bartol, Thomas M. and HETZER, Martin W and Tartakovsky, Daniel M. and Sejnowski, Terrence J.},
  issn         = {0006-3495},
  journal      = {Biophysical Journal},
  keywords     = {Biophysics},
  number       = {8},
  pages        = {1652--1660},
  publisher    = {Elsevier},
  title        = {{Anomalous diffusion of single particles in cytoplasm}},
  doi          = {10.1016/j.bpj.2013.01.049},
  volume       = {104},
  year         = {2013},
}

@article{10384,
  abstract     = {Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.},
  author       = {Mognetti, B. M. and Šarić, Anđela and Angioletti-Uberti, S. and Cacciuto, A. and Valeriani, C. and Frenkel, D.},
  issn         = {1079-7114},
  journal      = {Physical Review Letters},
  keywords     = {general physics and astronomy},
  number       = {24},
  publisher    = {American Physical Society},
  title        = {{Living clusters and crystals from low-density suspensions of active colloids}},
  doi          = {10.1103/physrevlett.111.245702},
  volume       = {111},
  year         = {2013},
}

@article{10385,
  abstract     = {We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.},
  author       = {Napoli, Joseph A. and Šarić, Anđela and Cacciuto, Angelo},
  issn         = {1744-6848},
  journal      = {Soft Matter},
  keywords     = {condensed matter physics, general chemistry},
  number       = {37},
  pages        = {8881--8886},
  publisher    = {Royal Society of Chemistry},
  title        = {{Collapsing nanoparticle-laden nanotubes}},
  doi          = {10.1039/c3sm51495a},
  volume       = {9},
  year         = {2013},
}

@article{10386,
  abstract     = {In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface.},
  author       = {Šarić, Anđela and Cacciuto, Angelo},
  issn         = {1744-6848},
  journal      = {Soft Matter},
  keywords     = {condensed matter physics, general chemistry},
  number       = {29},
  publisher    = {Royal Society of Chemistry},
  title        = {{Self-assembly of nanoparticles adsorbed on fluid and elastic membranes}},
  doi          = {10.1039/c3sm50188d},
  volume       = {9},
  year         = {2013},
}

@article{10396,
  abstract     = {Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.},
  author       = {Schlögl, Alois and Jonas, Peter M and Schmidt-Hieber, C. and Guzman, S. J.},
  issn         = {1862-278X},
  journal      = {Biomedical Engineering / Biomedizinische Technik},
  keywords     = {biomedical engineering, data analysis, free software},
  location     = {Graz, Austria},
  number       = {SI-1-Track-G},
  publisher    = {De Gruyter},
  title        = {{Stimfit: A fast visualization and analysis environment for cellular neurophysiology}},
  doi          = {10.1515/bmt-2013-4181},
  volume       = {58},
  year         = {2013},
}

@article{2107,
  abstract     = {We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes.},
  author       = {Skouras, Mélina and Thomaszewski, Bernhard and Coros, Stelian and Bickel, Bernd and Groß, Markus},
  journal      = {ACM Transactions on Graphics},
  number       = {4},
  publisher    = {ACM},
  title        = {{Computational design of actuated deformable characters}},
  doi          = {10.1145/2461912.2461979},
  volume       = {32},
  year         = {2013},
}

@article{2108,
  abstract     = {We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. },
  author       = {Coros, Stelian and Thomaszewski, Bernhard and Noris, Gioacchino and Sueda, Shinjiro and Forberg, Moira and Sumner, Robert W and Matusik, Wojciech and Bernd Bickel},
  journal      = {ACM Transactions on Graphics},
  number       = {4},
  publisher    = {ACM},
  title        = {{Computational design of mechanical characters}},
  doi          = {10.1145/2461912.2461953},
  volume       = {32},
  year         = {2013},
}

@article{2109,
  abstract     = {Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment.},
  author       = {Hildebrand, Kristian and Bernd Bickel and Alexa, Marc},
  journal      = {Computers and Graphics (Pergamon)},
  number       = {6},
  pages        = {669 -- 675},
  publisher    = {Elsevier},
  title        = {{Orthogonal slicing for additive manufacturing}},
  doi          = {10.1016/j.cag.2013.05.011},
  volume       = {37},
  year         = {2013},
}