@article{2791, abstract = {Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases. The transition from laminar to turbulent flow can involve a sequence of instabilities in which the system realizes progressively more complicated states, or it can occur suddenly. Once the transition has taken place, it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely. The flow of a fluid down a straight pipe provides a ubiquitous example of a shear flow undergoing a sudden transition from laminar to turbulent motion. Extensive calculations and experimental studies have shown that, at relatively low flow rates, turbulence in pipes is transient, and is characterized by an exponential distribution of lifetimes. They also suggest that for Reynolds numbers exceeding a critical value the lifetime diverges (that is, becomes infinitely large), marking a change from transient to persistent turbulence. Here we present experimental data and numerical calculations covering more than two decades of lifetimes, showing that the lifetime does not in fact diverge but rather increases exponentially with the Reynolds number. This implies that turbulence in pipes is only a transient event (contrary to the commonly accepted view), and that the turbulent and laminar states remain dynamically connected, suggesting avenues for turbulence control.}, author = {Björn Hof and Westerweel, Jerry and Schneider, Tobias M and Eckhardt, Bruno}, journal = {Nature}, number = {7107}, pages = {59 -- 62}, publisher = {Nature Publishing Group}, title = {{Finite lifetime of turbulence in shear flows}}, doi = {10.1038/nature05089}, volume = {443}, year = {2006}, } @article{2792, abstract = {Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4].}, author = {Björn Hof and van Doorne, Casimir W and Westerweel, Jerry and Nieuwstadt, Frans T}, journal = {Fluid Mechanics and its Applications}, pages = {109 -- 114}, publisher = {Springer}, title = {{Observation of nonlinear travelling waves in turbulent pipe flow}}, doi = {10.1007/1-4020-4159-4_11}, volume = {78}, year = {2006}, } @article{2894, abstract = {IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell.}, author = {Calado, Dinis P and Tiago Paixao and Holmberg, Dan and Haury, Matthias}, journal = {Journal of Immunology}, number = {8}, pages = {5358 -- 5364}, publisher = {American Association of Immunologists}, title = {{Stochastic Monoallelic Expression of IL 10 in T Cells}}, doi = {10.4049/jimmunol.177.8.5358 }, volume = {177}, year = {2006}, } @inbook{2921, abstract = {Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth.}, author = {Vladimir Kolmogorov and Zabih, Ramin}, booktitle = {Handbook of Mathematical Models in Computer Vision}, pages = {423 -- 427}, publisher = {Springer}, title = {{Graph cut algorithms for binocular stereo with occlusions}}, doi = {10.1007/0-387-28831-7_26}, year = {2006}, } @inbook{3002, abstract = {Arabidopsis thaliana is currently the most important model organism for basic molecular plant research. It is also a favourable model for developmental biology, as its embryogenesis follows a nearly invariant pattern of cell divisions and cell type specifications. Study of embryogenesis can involve genetic, physiological or biochemical approaches, but is always limited by the inaccessibility of the embryos which develop deep inside maternal tissue. Thus, for developmental studies, there is an increasing demand for methods which allow embryogenesis under artificial conditions, providing better accessibility to experimental manipulation. In this chapter, we address theoretical aspects of embryo culture, give some thoughts on which embryo culture system is suited best for which application and finally discuss three current methods which have been successfully used in Arabidopsis embryo culture. © 2006 Springer-Verlag Berlin Heidelberg.}, author = {Sauer, Michael and Jirí Friml}, booktitle = {Somatic Embryogenesis}, editor = {Mujib, Abdul and Šamaj, Jozef}, pages = {343 -- 354}, publisher = {Springer}, title = {{In vitro culture of Arabidopsis embryos}}, doi = {10.1007/7089_020}, volume = {2}, year = {2006}, } @article{3012, abstract = {Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.}, author = {Petrášek, Jan and Mravec, Jozef and Bouchard, Rodolphe and Blakeslee, Joshua and Melinda Abas and Seifertová, Daniela and Wiśniewska, Justyna and Tadele, Zerihun and Kubeš, Martin and Čovanová, Milada and Dhonukshe, Pankaj and Skůpa, Petr and Eva Benková and Perry, Lucie and Křeček, Pavel and Lee, Ok Ran and Fink, Gerald R and Geisler, Markus and Murphy, Angus S and Luschnig, Christian and Zažímalová, Eva and Jirí Friml}, journal = {Science}, number = {5775}, pages = {914 -- 918}, publisher = {American Association for the Advancement of Science}, title = {{PIN proteins perform a rate-limiting function in cellular auxin efflux}}, doi = {10.1126/science.1123542}, volume = {312}, year = {2006}, } @article{3010, abstract = {The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct "convergence points" in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning.}, author = {Scarpella, Enrico and Marcos, Danielle and Jirí Friml and Berleth, Thomas}, journal = {Genes and Development}, number = {8}, pages = {1015 -- 1027}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Control of leaf vascular patterning by polar auxin transport}}, doi = {10.1101/gad.1402406}, volume = {20}, year = {2006}, } @article{3007, abstract = {Root gravitropism describes the orientation of root growth along the gravity vector and is mediated by differential cell elongation in the root meristem. This response requires the coordinated, asymmetric distribution of the phytohormone auxin within the root meristem, and depends on the concerted activities of PIN proteins and AUX1 - members of the auxin transport pathway. Here, we show that intracellular trafficking and proteasome activity combine to control PIN2 degradation during root gravitropism. Following gravi-stimulation, proteasome-dependent variations in PIN2 localization and degradation at the upper and lower sides of the root result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a proteasome-dependent manner, indicating that the proteasome is involved in the control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution, and leads to defects in auxin distribution and gravitropic responses. We describe the effects of auxin on PIN2 localization and protein levels, indicating that redistribution of auxin during the gravitropic response may be involved in the regulation of PIN2 protein.}, author = {Abas, Lindy and Benjamins, René and Malenica, Nenad and Paciorek, Tomasz and Wiśniewska, Justyna and Moulinier-Anzola, Jeanette C and Sieberer, Tobias and Jirí Friml and Luschnig, Christian}, journal = {Nature Cell Biology}, number = {3}, pages = {249 -- 256}, publisher = {Nature Publishing Group}, title = {{Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism}}, doi = {10.1038/ncb1369}, volume = {8}, year = {2006}, } @article{3006, abstract = {Dividing plant cells perform a remarkable task of building a new cell wall within the cytoplasm in a few minutes. A long-standing paradigm claims that this primordial cell wall, known as the cell plate, is generated by delivery of newly synthesized material from Golgi apparatus-originated secretory vesicles. Here, we show that, in diverse plant species, cell surface material, including plasma membrane proteins, cell wall components, and exogenously applied endocytic tracers, is rapidly delivered to the forming cell plate. Importantly, this occurs even when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced during cell plate formation, and its genetic or pharmacological inhibition leads to cytokinesis defects. Our results reveal that endocytic delivery of cell surface material significantly contributes to cell plate formation during plant cytokinesis. }, author = {Dhonukshe, Pankaj and Baluška, František and Schlicht, Markus and Hlavacka, Andrej and Šamaj, Jozef and Jirí Friml and Gadella, Theodorus W}, journal = {Developmental Cell}, number = {1}, pages = {137 -- 150}, publisher = {Cell Press}, title = {{Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis}}, doi = {10.1016/j.devcel.2005.11.015}, volume = {10}, year = {2006}, } @article{3011, abstract = {Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity.}, author = {Wiśniewska, Justyna and Xu, Jian and Seifertová, Daniela and Brewer, Philip B and Růžička, Kamil and Blilou, Ikram and Rouquié, David and Eva Benková and Scheres, Ben and Jirí Friml}, journal = {Science}, number = {5775}, publisher = {American Association for the Advancement of Science}, title = {{Polar PIN localization directs auxin flow in plants}}, doi = {10.1126/science.1121356}, volume = {312}, year = {2006}, } @article{3005, author = {Friml, Jirí and Benfey, Philip and Benková, Eva and Bennett, Malcolm and Berleth, Thomas and Geldner, Niko and Grebe, Markus and Heisler, Marcus and Hejátko, Jan and Jürgens, Gerd and Laux, Thomas and Lindsey, Keith and Lukowitz, Wolfgang and Luschnig, Christian and Offringa, Remko and Scheres, Ben and Swarup, Ranjan and Torres Ruiz, Ramón and Weijers, Dolf and Zažímalová, Eva}, journal = {Trends in Plant Science}, number = {1}, pages = {12 -- 14}, publisher = {Cell Press}, title = {{Apical-basal polarity: Why plant cells don't stand on their heads}}, doi = {10.1016/j.tplants.2005.11.010}, volume = {11}, year = {2006}, } @article{3008, abstract = {Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.}, author = {Xu, Jian and Hofhuis, Hugo and Heidstra, Renze and Sauer, Michael and Jirí Friml and Scheres, Ben}, journal = {Science}, number = {5759}, pages = {385 -- 388}, publisher = {American Association for the Advancement of Science}, title = {{A molecular framework for plant regeneration}}, doi = {10.1126/science.1121790}, volume = {311}, year = {2006}, } @article{3009, author = {Paciorek, Tomasz and Friml, Jirí}, journal = {Journal of Cell Science}, number = {7}, pages = {1199 -- 1202}, publisher = {Company of Biologists}, title = {{Auxin signaling}}, doi = {10.1242/jcs.02910}, volume = {119}, year = {2006}, } @article{3016, abstract = {Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants.}, author = {Sauer, Michael and Balla, Jozef and Luschnig, Christian and Wiśniewska, Justyna and Reinöhl, Vilém and Friml, Jirí and Benková, Eva}, journal = {Genes and Development}, number = {20}, pages = {2902 -- 2911}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity}}, doi = {10.1101/gad.390806}, volume = {20}, year = {2006}, } @article{3017, abstract = {The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.}, author = {Tanaka, Hirokazu and Dhonukshe, Pankaj and Brewer, Philip and Friml, Jirí}, journal = {Cellular and Molecular Life Sciences}, number = {23}, pages = {2738 -- 2754}, publisher = {Birkhäuser}, title = {{Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development}}, doi = {10.1007/s00018-006-6116-5}, volume = {63}, year = {2006}, } @article{3018, abstract = {The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport.}, author = {Kleine-Vehn, Jürgen and Dhonukshe, Pankaj and Swarup, Ranjan and Bennett, Malcolm and Jirí Friml}, journal = {Plant Cell}, number = {11}, pages = {3171 -- 3181}, publisher = {American Society of Plant Biologists}, title = {{Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1}}, doi = {10.1105/tpc.106.042770}, volume = {18}, year = {2006}, } @article{3020, abstract = {High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used.}, author = {Hejátko, Jan and Blilou, Ikram and Brewer, Philip B and Jirí Friml and Scheres, Ben and Eva Benková}, journal = {Nature Protocols}, number = {4}, pages = {1939 -- 1946}, publisher = {Nature Publishing Group}, title = {{In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples}}, doi = {10.1038/nprot.2006.333}, volume = {1}, year = {2006}, } @article{3015, abstract = {As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.}, author = {Sauer, Michael and Paciorek, Tomasz and Eva Benková and Jirí Friml}, journal = {Nature Protocols}, number = {1}, pages = {98 -- 103}, publisher = {Nature Publishing Group}, title = {{Immunocytochemical techniques for whole mount in situ protein localization in plants}}, doi = {10.1038/nprot.2006.15}, volume = {1}, year = {2006}, } @article{3013, abstract = {There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications.}, author = {Paciorek, Tomasz and Sauer, Michael and Balla, Jozef and Wiśniewska, Justyna and Jirí Friml}, journal = {Nature Protocols}, number = {1}, pages = {104 -- 107}, publisher = {Nature Publishing Group}, title = {{Immunocytochemical technique for protein localization in sections of plant tissues}}, doi = {10.1038/nprot.2006.16}, volume = {1}, year = {2006}, } @article{3014, abstract = {Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days.}, author = {Brewer, Philip B and Heisler, Marcus G and Hejátko, Jan and Jirí Friml and Eva Benková}, journal = {Nature Protocols}, number = {3}, pages = {1462 -- 1467}, publisher = {Nature Publishing Group}, title = {{In situ hybridization for mRNA detection in Arabidopsis tissue sections}}, doi = {10.1038/nprot.2006.226}, volume = {1}, year = {2006}, } @article{3152, abstract = {The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms.}, author = {Kunwar, Prabhat S and Daria Siekhaus and Lehmann, Ruth}, journal = {Annual Review of Cell and Developmental Biology}, pages = {237 -- 265}, publisher = {Annual Reviews}, title = {{In vivo migration A germ cell perspective}}, doi = {10.1146/annurev.cellbio.22.010305.103337}, volume = {22}, year = {2006}, } @inproceedings{3189, abstract = {This paper presents an algorithm capable of real-time separation of foreground from background in monocular video sequences. Automatic segmentation of layers from colour/contrast or from motion alone is known to be error-prone. Here motion, colour and contrast cues are probabilistically fused together with spatial and temporal priors to infer layers accurately and efficiently. Central to our algorithm is the fact that pixel velocities are not needed, thus removing the need for optical flow estimation, with its tendency to error and computational expense. Instead, an efficient motion vs non-motion classifier is trained to operate directly and jointly on intensity-change and contrast. Its output is then fused with colour information. The prior on segmentation is represented by a second order, temporal, Hidden Markov Model, together with a spatial MRF favouring coherence except where contrast is high. Finally, accurate layer segmentation and explicit occlusion detection are efficiently achieved by binary graph cut. The segmentation accuracy of the proposed algorithm is quantitatively evaluated with respect to existing ground-truth data and found to be comparable to the accuracy of a state of the art stereo segmentation algorithm. Fore-ground/background segmentation is demonstrated in the application of live background substitution and shown to generate convincingly good quality composite video.}, author = {Criminisi, Antonio and Cross, Geoffrey and Blake, Andrew and Vladimir Kolmogorov}, pages = {53 -- 60}, publisher = {IEEE}, title = {{Bilayer segmentation of live video}}, doi = {10.1109/CVPR.2006.69}, volume = {1}, year = {2006}, } @article{3190, abstract = {Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. (Nov. 2005)- tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound - it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in (M. J. Wainwright, et al., Nov. 2005). In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts.}, author = {Vladimir Kolmogorov}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {10}, pages = {1568 -- 1583}, publisher = {IEEE}, title = {{Convergent tree reweighted message passing for energy minimization}}, doi = {10.1109/TPAMI.2006.200}, volume = {28}, year = {2006}, } @inproceedings{3188, abstract = {We introduce the term cosegmentation which denotes the task of segmenting simultaneously the common parts of an image pair. A generative model for cosegmentation is presented. Inference in the model leads to minimizing an energy with an MRF term encoding spatial coherency and a global constraint which attempts to match the appearance histograms of the common parts. This energy has not been proposed previously and its optimization is challenging and NP-hard. For this problem a novel optimization scheme which we call trust region graph cuts is presented. We demonstrate that this framework has the potential to improve a wide range of research: Object driven image retrieval, video tracking and segmentation, and interactive image editing. The power of the framework lies in its generality, the common part can be a rigid/non-rigid object (or scene), observed from different viewpoints or even similar objects of the same class.}, author = {Rother, Carsten and Vladimir Kolmogorov and Minka, Thomas P and Blake, Andrew}, pages = {993 -- 1000}, publisher = {IEEE}, title = {{Cosegmentation of image pairs by histogram matching - Incorporating a global constraint into MRFs}}, doi = {10.1109/CVPR.2006.91}, year = {2006}, } @inproceedings{3214, abstract = {The Feistel-network is a popular structure underlying many block-ciphers where the cipher is constructed from many simpler rounds, each defined by some function which is derived from the secret key. Luby and Rackoff showed that the three-round Feistel-network – each round instantiated with a pseudorandom function secure against adaptive chosen plaintext attacks (CPA) – is a CPA secure pseudorandom permutation, thus giving some confidence in the soundness of using a Feistel-network to design block-ciphers. But the round functions used in actual block-ciphers are – for efficiency reasons – far from being pseudorandom. We investigate the security of the Feistel-network against CPA distinguishers when the only security guarantee we have for the round functions is that they are secure against non-adaptive chosen plaintext attacks (nCPA). We show that in the information-theoretic setting, four rounds with nCPA secure round functions are sufficient (and necessary) to get a CPA secure permutation. Unfortunately, this result does not translate into the more interesting pseudorandom setting. In fact, under the so-called Inverse Decisional Diffie-Hellman assumption the Feistel-network with four rounds, each instantiated with a nCPA secure pseudorandom function, is in general not a CPA secure pseudorandom permutation.}, author = {Maurer, Ueli M and Oswald, Yvonne A and Krzysztof Pietrzak and Sjödin, Johan}, pages = {391 -- 408}, publisher = {Springer}, title = {{Luby Rackoff ciphers from weak round functions }}, doi = {10.1007/11761679_24}, volume = {4004}, year = {2006}, } @inproceedings{3215, abstract = {Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.}, author = {Dodis, Yevgeniy and Krzysztof Pietrzak and Przydatek, Bartosz}, pages = {601 -- 616}, publisher = {Springer}, title = {{Separating sources for encryption and secret sharing}}, doi = {10.1007/11681878_31}, volume = {3876}, year = {2006}, } @inproceedings{3217, abstract = {To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true. To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not.}, author = {Krzysztof Pietrzak}, pages = {328 -- 338}, publisher = {Springer}, title = {{Composition implies adaptive security in minicrypt}}, doi = {10.1007/11761679_20}, volume = {4004}, year = {2006}, } @inproceedings{3216, abstract = {We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04]. The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found.}, author = {Krzysztof Pietrzak}, pages = {168 -- 179}, publisher = {Springer}, title = {{A tight bound for EMAC}}, doi = {10.1007/11787006_15}, volume = {4052}, year = {2006}, } @article{3522, abstract = {We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs.}, author = {Joseph O'Neill and Senior,Timothy and Jozsef Csicsvari}, journal = {Neuron}, number = {1}, pages = {143 -- 155}, publisher = {Elsevier}, title = {{Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior}}, doi = {10.1016/j.neuron.2005.10.037}, volume = {49}, year = {2006}, } @article{3607, abstract = {We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences.}, author = {Turelli, Michael and Nicholas Barton}, journal = {Evolution; International Journal of Organic Evolution}, number = {9}, pages = {1763 -- 1776}, publisher = {Wiley-Blackwell}, title = {{Will population bottlenecks and multilocus epistasis increase additive genetic variance?}}, doi = {10.1111/j.0014-3820.2006.tb00521.x}, volume = {60}, year = {2006}, } @inproceedings{3683, abstract = {Many algorithms to remove distortion from document images have be proposed in recent years, but so far there is no reliable method for comparing their performance. In this paper we propose a collection of methods to measure the quality of such restoration algorithms for document image which show a non-linear distortion due to perspective or page curl. For the result from these measurement to be meaningful, a common data set of ground truth is required. We therefore started with the buildup of a document image database that is meant to serve as a common data basis for all kinds of restoration from images of 3D-shaped document. The long term goal would be to establish this database and following extensions in the area of document image dewarping as an as fruitful and indispensable tool as e.g. the NIST database is for OCR, or the Caltech database is for object and face recognition.}, author = {Christoph Lampert and Breuel,Thomas M}, publisher = {Springer}, title = {{Objective quality measurement for geometric document image restoration}}, year = {2006}, } @inproceedings{3685, abstract = {Video compression currently is dominated by engineering and fine-tuned heuristic methods. In this paper, we propose to instead apply the well-developed machinery of machine learning in order to support the optimization of existing video encoders and the creation of new ones. Exemplarily, we show how by machine learning we can improve one encoding step that is crucial for the performance of all current video standards: macroblock mode decision. By formulating the problem in a Bayesian setup, we show that macroblock mode decision can be reduced to a classification problem with a cost function for misclassification that is sample dependent. We demonstrate how to apply different machine learning techniques to obtain suitable classifiers and we show in detailed experiments that all of these perform better than the state-of-the-art heuristic method}, author = {Christoph Lampert}, pages = {936 -- 940}, publisher = {IEEE}, title = {{Machine learning for video compression: Macroblock mode decision}}, doi = {10.1109/ICPR.2006.778}, year = {2006}, } @article{3750, abstract = {We applied a single-cell assay to characterize how transcription dynamics affects protein expression levels of a tetracycline-inducible gene expression system. Transcriptional activity of the tetracycline promoter in response to a steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype Escherichia coli cells. We found that the expression level of the green fluorescent protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells.}, author = {Le,Thuc T. and Calin Guet and Cluzel,Philippe}, journal = {Protein Expression and Purification}, number = {1}, pages = {28 -- 31}, publisher = {Elsevier}, title = {{Protein expression enhancement in efflux-deleted mutant bacteria}}, volume = {48}, year = {2006}, } @article{3767, abstract = {Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search.}, author = {Anne Kupczok and Dittrich,Peter}, journal = {Journal of Theoretical Biology}, number = {3}, pages = {726 -- 35}, publisher = {Elsevier}, title = {{Determinants of simulated RNA evolution.}}, doi = {10.1016/j.jtbi.2005.06.019}, volume = {238}, year = {2006}, } @article{3813, abstract = {Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus.}, author = {Aponte, Yexica and Lien, Cheng-Chang and Reisinger, Ellen and Peter Jonas}, journal = {Journal of Physiology}, number = {Pt 1}, pages = {229 -- 43}, publisher = {Wiley-Blackwell}, title = {{Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus}}, doi = {10.1113/jphysiol.2005.104042}, volume = {574}, year = {2006}, } @misc{3814, abstract = {The axon terminals (mossy fibers) of hippocampal dentate granule cells form characteristic synaptic connections with large spines or excrescences of both hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled mossy fibers and immunolabeling of target cells with interneuron markers has revealed that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic inhibitory interneurons rather than to excitatory principal cells, although the functional implications of these quantitative differences are unclear. Following a brief description of the "classical" mossy fiber synapse on excrescences of CA3 pyramidal cells, the present review focuses on the contacts formed between granule cells and GABAergic interneurons, both normally and after synaptic reorganization. In response to deafferentation of mossy cell target cells, which include both granule cells and interneurons, mossy fibers "sprout" new axon collaterals that form a band of supragranular mossy fibers in the inner molecular layer of the dentate gyrus. Although most newly formed recurrent mossy fibers establish synapses with granule cells, there is an apparently convergent input of new mossy fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are observed in chronically epileptic rats and may be the structural correlate of the granule cell hyperinhibition observed in these animals in vivo. Together, the findings reviewed here establish mossy fiber synapses as an important component of inhibitory circuits in the hippocampus.}, author = {Frotscher, Michael and Peter Jonas and Sloviter, Robert S}, booktitle = {Cell and Tissue Research}, number = {2}, pages = {361 -- 7}, publisher = {Springer}, title = {{Synapses formed by normal and abnormal hippocampal mossy fibers (Review)}}, doi = {10.1007/s00441-006-0269-2}, volume = {326}, year = {2006}, } @article{3815, abstract = {It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.}, author = {Bischofberger, Josef and Engel, Dominique and Frotscher, Michael and Peter Jonas}, journal = {Pflugers Archiv : European Journal of Physiology}, number = {3}, pages = {361 -- 72}, publisher = {Springer}, title = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network}}, doi = {10.1007/s00424-006-0093-2}, volume = {453}, year = {2006}, } @article{3811, abstract = {Networks of GABAergic neurons are key elements in the generation of gamma oscillations in the brain. Computational studies suggested that the emergence of coherent oscillations requires hyperpolarizing inhibition. Here, we show that GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting inhibition is incorporated into a structured interneuron network model with fast and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing inhibition, networks with shunting inhibition show several advantages. First, oscillations are generated with smaller tonic excitatory drive. Second, network frequencies are tuned to the gamma band. Finally, robustness against heterogeneity in the excitatory drive is markedly improved. In single interneurons, shunting inhibition shortens the interspike interval for low levels of drive but prolongs it for high levels, leading to homogenization of neuronal firing rates. Thus, shunting inhibition may confer increased robustness to gamma oscillations in the brain.}, author = {Vida, Imre and Bartos, Marlene and Peter Jonas}, journal = {Neuron}, number = {1}, pages = {107 -- 17}, publisher = {Elsevier}, title = {{Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates}}, doi = {10.1016/j.neuron.2005.11.036}, volume = {49}, year = {2006}, } @article{3817, author = {Frotscher, Michael and Gundelfinger, Eckart and Peter Jonas and Neher, Erwin and Seeburg, Peter}, journal = {Cell and Tissue Research}, number = {2}, pages = {203 -- 4}, publisher = {Springer}, title = {{The most important recent advances in synapse research from my point of view--and what remains to be done}}, doi = {10.1007/s00441-006-0325-y}, volume = {326}, year = {2006}, } @article{3912, abstract = {Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony.}, author = {Cremer, Sylvia and Ugelvig, Line V and Lommen, Suzanne and Petersen, Klaus and Pedersen, Jes}, journal = {Myrmecological News}, pages = {13 -- 19}, publisher = {Österreichische Gesellschaft für Entomofaunistik}, title = {{Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain}}, volume = {9}, year = {2006}, } @article{3914, abstract = {We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable.}, author = {Moder, Karl and Schlick Steiner, Birgit and Steiner, Florian and Cremer, Sylvia and Christian, Erhard and Seifert, Bernhard}, journal = {Journal of Zoological Systematics and Evolutionary Research}, number = {1}, pages = {82 -- 87}, publisher = {Wiley-Blackwell}, title = {{Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study}}, doi = {10.1111/j.1439-0469.2006.00372.x}, volume = {45}, year = {2006}, } @article{3913, abstract = {Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention.}, author = {Heinze, Jürgen and Cremer, Sylvia and Eckl, Norbert and Schrempf, Alexandra}, journal = {Insectes Sociaux}, number = {1}, pages = {1 -- 7}, publisher = {Springer}, title = {{Stealthy invaders: the biology of Cardiocondyla tramp ants}}, doi = {10.1007/s00040-005-0847-4}, volume = {53}, year = {2006}, } @article{3932, abstract = {OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.}, author = {Henic, Emir and Michael Sixt and Hansson, Stefan and Høyer-Hansen, Gunilla and Casslén, Bertil}, journal = {Gynecologic Oncology}, number = {1}, pages = {28 -- 39}, publisher = {Elsevier}, title = {{EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor}}, doi = {10.1016/j.ygyno.2005.09.038}, volume = {101}, year = {2006}, } @article{3978, abstract = {Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures.}, author = {Ban, Yih-En Andrew and Rudolph, Johannes and Zhou, Pei and Herbert Edelsbrunner}, journal = {Proteins: Structure, Function and Bioinformatics}, number = {4}, pages = {852 -- 864}, publisher = {Wiley-Blackwell}, title = {{Evaluating the quality of NMR structures by local density of protons}}, doi = {10.1002/prot.20811}, volume = {62}, year = {2006}, } @article{3979, abstract = {Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.}, author = {Ban, Yih-En Andrew and Herbert Edelsbrunner and Rudolph, Johannes}, journal = {Journal of the ACM}, number = {3}, pages = {361 -- 378}, publisher = {ACM}, title = {{Interface surfaces for protein-protein complexes}}, doi = {10.1145/1147954.1147957}, volume = {53}, year = {2006}, } @article{3980, abstract = {Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.}, author = {Agarwal, Pankaj K and Herbert Edelsbrunner and Harer, John and Wang, Yusu}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {553 -- 572}, publisher = {Springer}, title = {{Extreme elevation on a 2-manifold}}, doi = {10.1007/s00454-006-1265-8}, volume = {36}, year = {2006}, } @article{4345, abstract = {Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert.}, author = {Patrick Danowski and Heller,Lambert}, journal = {Bibliotheksdienst}, number = {11}, pages = {1250 -- 1271}, publisher = {Zentral- und Landesbibliothek Berlin}, title = {{Bibliothek 2.0 - Die Bibliothek der Zukunft?}}, doi = {424}, volume = {40}, year = {2006}, } @article{4352, abstract = {Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.}, author = {Conn, Jan E and Vineis, Joseph H and Jonathan Bollback and Onyabe, David Y and Wilkerson, Richard C and Povoa, Marinete M}, journal = {The American Journal of Tropical Medicine and Hygiene}, number = {5}, pages = {798 -- 806}, publisher = {American Society of Tropical Medicine and Hygiene}, title = {{Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil}}, volume = {74}, year = {2006}, } @article{4351, abstract = {BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.}, author = {Jonathan Bollback}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, title = {{SIMMAP: stochastic character mapping of discrete traits on phylogenies}}, doi = {10.1186/1471-2105-7-88}, volume = {7}, year = {2006}, } @inproceedings{3180, abstract = {One of the most exciting advances in early vision has been the development of efficient energy minimization algorithms. Many early vision tasks require labeling each pixel with some quantity such as depth or texture. While many such problems can be elegantly expressed in the language of Markov Random Fields (MRF's), the resulting energy minimization problems were widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. Unfortunately, most papers define their own energy function, which is minimized with a specific algorithm of their choice. As a result, the tradeoffs among different energy minimization algorithms are not well understood. In this paper we describe a set of energy minimization benchmarks, which we use to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods - graph cuts, LBP, and tree-reweighted message passing - as well as the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching and interactive segmentation. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods with minimal overhead. We expect that the availability of our benchmarks and interface will make it significantly easier for vision researchers to adopt the best method for their specific problems. Benchmarks, code, results and images are available at http://vision.middlebury.edu/MRF.}, author = {Szeliski, Richard S and Zabih, Ramin and Scharstein, Daniel and Veksler, Olga and Vladimir Kolmogorov and Agarwala, Aseem and Tappen, Marshall F and Rother, Carsten}, pages = {16 -- 29}, publisher = {Springer}, title = {{A comparative study of energy minimization methods for Markov random fields}}, doi = {10.1007/11744047_2}, volume = {3952}, year = {2006}, } @inproceedings{3184, abstract = {Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.}, author = {Vladimir Kolmogorov and Rother, Carsten}, pages = {1 -- 15}, publisher = {Springer}, title = {{Comparison of energy minimization algorithms for highly connected graphs}}, doi = {10.1007/11744047_1}, volume = {3952 LNCS}, year = {2006}, } @article{3185, abstract = {This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.}, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {9}, pages = {1480 -- 1492}, publisher = {IEEE}, title = {{Probabilistic fusion of stereo with color and contrast for bilayer segmentation}}, doi = {10.1109/TPAMI.2006.193}, volume = {28}, year = {2006}, } @inproceedings{3186, abstract = {We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion.}, author = {Boykov, Yuri and Vladimir Kolmogorov and Cremers, Daniel and Delong, Andrew}, pages = {409 -- 422}, publisher = {Springer}, title = {{An integral solution to surface evolution PDEs via geo cuts}}, doi = {10.1007/11744078_32}, volume = {3953}, year = {2006}, } @inbook{3404, author = {Harald Janovjak and Sawhney, Ravi K and Stark, Martin and Mueller, Daniel J}, booktitle = {Techniques in Microscopy for Biomedical Applications}, pages = {213 -- 284}, publisher = {World Scientific Publishing}, title = {{Atomic force microscopy}}, volume = {2}, year = {2006}, } @article{3413, abstract = {Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.}, author = {Kessler, Max and Gottschalk, Kay E and Harald Janovjak and Mueller, Daniel J and Gaub, Hermann}, journal = {Journal of Molecular Biology}, number = {2}, pages = {644 -- 654}, publisher = {Elsevier}, title = {{Bacteriorhodopsin folds into the membrane against an external force}}, doi = {10.1016/j.jmb.2005.12.065}, volume = {357}, year = {2006}, } @article{3414, abstract = {Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter.}, author = {Kedrov, Alexej and Harald Janovjak and Ziegler, Christine and Kühlbrandt, Werner and Mueller, Daniel J}, journal = {Journal of Molecular Biology}, number = {1}, pages = {2 -- 8}, publisher = {Elsevier}, title = {{Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli}}, doi = {10.1016/j.jmb.2005.10.028}, volume = {355}, year = {2006}, } @misc{3415, author = {Harald Janovjak and Kedrov, Alexej and Cisneros, David and Sapra, Tanuj K and Struckmeier, Jens and Mueller, Daniel J}, booktitle = {Neurobiology of Aging}, pages = {546 -- 561}, publisher = {Elsevier}, title = {{Imaging and detecting molecular interactions of single membrane proteins}}, doi = {10.1016/j.neurobiolaging.2005.03.031}, volume = {27}, year = {2006}, } @article{3437, abstract = {The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.}, author = {Betancourt, Andrea J and Jonathan Bollback}, journal = {Current Opinion in Genetics & Development}, number = {6}, pages = {618 -- 623}, publisher = {Elsevier}, title = {{Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution}}, doi = {10.1016/j.gde.2006.10.006}, volume = {16}, year = {2006}, } @unpublished{3431, abstract = {Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.}, author = {Gasper Tkacik and Schneidman, E. and Berry, M. J. and Bialek, William S}, booktitle = {ArXiv}, pages = {1 -- 4}, publisher = {ArXiv}, title = {{Ising models for networks of real neurons}}, year = {2006}, } @inproceedings{3449, abstract = {We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.}, author = {Krishnendu Chatterjee and Jagadeesan, Rhada and Pitcher, Corin}, pages = {70 -- 82}, publisher = {IEEE}, title = {{Games for controls}}, doi = {10.1109/CSFW.2006.14}, year = {2006}, } @misc{3463, abstract = {It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network.}, author = {Bischofberger, Joseph and Engel, Dominique and Frotscher, Michael and Peter Jonas}, booktitle = {Pflugers Archiv : European Journal of Physiology}, number = {3}, pages = {361 -- 372}, publisher = {Springer}, title = {{Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)}}, doi = {10.1007/s00424-006-0093-2}, volume = {453}, year = {2006}, } @inproceedings{3499, abstract = {We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε>0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. }, author = {Krishnendu Chatterjee}, pages = {271 -- 286}, publisher = {Springer}, title = {{Nash equilibrium for upward-closed objectives}}, doi = {10.1007/11874683_18}, volume = {4207}, year = {2006}, } @inproceedings{3500, abstract = {The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n).}, author = {Krishnendu Chatterjee and Thomas Henzinger and Piterman, Nir}, publisher = {ACM}, title = {{Algorithms for Büchi Games}}, year = {2006}, } @misc{3510, abstract = {Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation.}, author = {Edelsbrunner, Herbert and Fu, Ping and Nekhayev, Dmitry and Facello, Michael and Williams, Steven}, title = {{Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism}}, year = {2006}, } @misc{3511, abstract = {Methods, apparatus and computer program products provide efficient techniques for designing and printing shells of hearing-aid devices with a high degree of quality assurance and reliability and with a reduced number of manual and time consuming production steps and operations. These techniques also preferably provide hearing-aid shells having internal volumes that can approach a maximum allowable ratio of internal volume relative to external volume. These high internal volumes facilitate the inclusion of hearing-aid electrical components having higher degrees of functionality and/or the use of smaller and less conspicuous hearing-aid shells. A preferred method includes operations to generate a watertight digital model of a hearing-aid shell by thickening a three-dimensional digital model of a shell surface in a manner that eliminates self-intersections and results in a thickened model having an internal volume that is a high percentage of an external volume of the model. }, author = {Fu, Ping and Nekhayev, Dmitry and Edelsbrunner, Herbert}, title = {{Manufacturing methods and systems for rapid production of hearing-aid shells}}, year = {2006}, } @misc{3512, abstract = {Methods, apparatus and computer program products provide efficient techniques for reconstructing surfaces from data point sets. These techniques include reconstructing surfaces from sets of scanned data points that have preferably undergone preprocessing operations to improve their quality by, for example, reducing noise and removing outliers. These techniques include reconstructing a dense and locally two-dimensionally distributed 3D point set (e.g., point cloud) by merging stars in two-dimensional weighted Delaunay triangulations within estimated tangent planes. The techniques include determining a plurality of stars from a plurality of points p.sub.i in a 3D point set S that at least partially describes the 3D surface, by projecting the plurality of points p.sub.i onto planes T.sub.i that are each estimated to be tangent about a respective one of the plurality of points p.sub.i. The plurality of stars are then merged into a digital model of the 3D surface.}, author = {Fletcher, Yates and Gloth, Tobias and Edelsbrunner, Herbert and Fu, Ping}, title = {{Method, apparatus and computer products that reconstruct surfaces from data points}}, year = {2006}, } @article{3545, abstract = {The functional organization of the basal ganglia ( BG) is often defined according to one of two opposing schemes. The first proposes multiple, essentially independent channels of information processing. The second posits convergence and lateral integration of striatal channels at the level of the globus pallidus ( GP). We tested the hypothesis that these proposed aspects of functional connectivity within the striatopallidal axis are dynamic and related to brain state. Local field potentials ( LFPs) were simultaneously recorded from multiple sites in striatum and GP in anesthetized rats during slow-wave activity( SWA) and during global activation evoked by sensory stimulation. Functional connectivity was inferred from comparative analyses of the internuclear and intranuclear coherence between bipolar derivations of LFPs. During prominent SWA, as shown in the electrocorticogram and local field potentials in the basal ganglia, intranuclear coherence, and, thus, lateral functional connectivity within striatum or globus pallidus was relatively weak. Furthermore, the temporal coupling of LFPs recorded across these two nuclei involved functional convergence at the level of GP. Global activation, indicated by a loss of SWA, was accompanied by a rapid functional reorganization of the striatopallidal axis. Prominent lateral functional connectivity developed within GP and, to a significantly more constrained spatial extent, striatum. Additionally, functional convergence on GP was no longer apparent, despite increased internuclear coherence. These data demonstrate that functional connectivity within the BG is highly dynamic and suggest that the relative expression of organizational principles, such as parallel, independent processing channels, striatopallidal convergence, and lateral integration within BG nuclei, is dependent on brain state.}, author = {Magill,Peter J and Pogosyan,Alek and Sharott,Andrew and Jozsef Csicsvari and Bolam, John Paul and Brown,Peter}, journal = {Journal of Neuroscience}, number = {23}, pages = {6318 -- 6329}, publisher = {Society for Neuroscience}, title = {{Changes in functional connectivity within the rat striatopallidal axis during global brain activation in vivo}}, doi = {10.1523/​JNEUROSCI.0620-06.2006}, volume = {26}, year = {2006}, } @inproceedings{3559, abstract = {Persistent homology is the mathematical core of recent work on shape, including reconstruction, recognition, and matching. Its per- tinent information is encapsulated by a pairing of the critical values of a function, visualized by points forming a diagram in the plane. The original algorithm in [10] computes the pairs from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. The main result of this paper is an algorithm that maintains the pairing in worst-case linear time per transposition in the ordering. A side-effect of the algorithm’s anal- ysis is an elementary proof of the stability of persistence diagrams [7] in the special case of piecewise-linear functions. We use the algorithm to compute 1-parameter families of diagrams which we apply to the study of protein folding trajectories.}, author = {Cohen-Steiner, David and Herbert Edelsbrunner and Morozov, Dmitriy}, pages = {119 -- 126}, publisher = {ACM}, title = {{Vines and vineyards by updating persistence in linear time}}, doi = {10.1145/1137856.1137877}, year = {2006}, } @inproceedings{3560, abstract = {We continue the study of topological persistence [5] by investigat- ing the problem of simplifying a function f in a way that removes topological noise as determined by its persistence diagram [2]. To state our results, we call a function g an ε-simplification of another function f if ∥f − g∥∞ ≤ ε, and the persistence diagrams of g are the same as those of f except all points within L1-distance at most ε from the diagonal have been removed. We prove that for func- tions f on a 2-manifold such ε-simplification exists, and we give an algorithm to construct them in the piecewise linear case.}, author = {Herbert Edelsbrunner and Morozov, Dmitriy and Pascucci, Valerio}, pages = {127 -- 134}, publisher = {ACM}, title = {{Persistence-sensitive simplification of functions on 2-manifolds}}, doi = {10.1145/1137856.1137878}, year = {2006}, } @misc{3594, author = {Pemberton, Josephine M and Swanson, Graeme M and Nicholas Barton and Livingstone, Suzanne R and Senn, Helen V}, booktitle = {Deer}, number = {9}, pages = {22 -- 26}, publisher = {BDS }, title = {{Hybridisation between red and sika deer in Scotland}}, volume = {13}, year = {2006}, } @article{3609, abstract = {Bombina bombina and B. variegata are two anciently diverged toad taxa that have adapted to different breeding habitats yet hybridize freely in zones of overlap where their parapatric distributions meet. Here, we report on a joint genetic and ecological analysis of a hybrid zone in the vicinity of Stryi in western Ukraine. We used five unlinked allozyme loci, two nuclear single nucleotide polymorphisms and a mitochondrial DNA haplotype as genetic markers. Parallel allele frequency clines with a sharp central step occur across a sharp ecotone, where transitions in aquatic habitat, elevation, and terrestrial vegetation coincide. The width of the hybrid zone, estimated as the inverse of the maximum gradient in allele frequency, is 2.3 km. This is the smallest of four estimates derived from different clinal transects across Europe. We argue that the narrow cline near Stryi is mainly due to a combination of habitat distribution and habitat preference. Adult toads show a preference for either ponds (B. bombina) or puddles (B. variegata), which is known to affect the distribution of genotypes within the hybrid zones. At Stryi, it should cause a reduction of the dispersal rate across the ecotone and thus narrow the cline. A detailed comparison of all five intensively studied Bombina transects lends support to the hypothesis that habitat distribution plus habitat preference can jointly affect the structure of hybrid zones and, ultimately, the resulting barriers to gene flow between differentiated gene pools. This study also represents a resampling of an area that was last studied more than 70 years ago. Our allele-frequency clines largely coincide with those that were described then on the basis of morphological variation. However, we found asymmetrical introgression of B. variegata genes into B. bombina territory along the bank of a river.}, author = {Yanchukov, Alexey and Hofman, Sebastian and Szymura, Jacek M and Mezhzherin, Sergey V and Morozov-Leonov, Sviatoslav and Nicholas Barton and Nürnberger, Beate}, journal = {Evolution; International Journal of Organic Evolution}, number = {3}, pages = {583 -- 600}, publisher = {Wiley-Blackwell}, title = {{Hybridization of Bombina bombina and B. variegata (Anura, Discoglossidae) at a sharp ecotone in western Ukraine: comparisons across transects and over time}}, doi = {10.1111/j.0014-3820.2006.tb01139.x}, volume = {60}, year = {2006}, } @article{3608, abstract = {We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests. }, author = {Kirkpatrick, Mark and Nicholas Barton}, journal = {Genetics}, number = {1}, pages = {419 -- 434}, publisher = {Genetics Society of America}, title = {{Chromosome inversions, local adaptation, and speciation}}, doi = {10.1534/genetics.105.047985}, volume = {173}, year = {2006}, } @article{3610, abstract = {For a model of diallelic loci with arbitrary epistasis, Barton and Turelli [2004. Effects of genetic drift on variance components under a general model of epistasis. Evolution 58, 2111–2132] gave results for variances among and within replicate lines obtained by inbreeding without selection. Here, we discuss the relation between their population genetic methods and classical quantitative genetic arguments. In particular, we consider the case of no dominance using classical identity by descent arguments, which generalizes their results from two alleles to multiple alleles. To clarify the connections between the alternative methods, we obtain the same results using an intermediate method, which explicitly identifies the statistical effects of sets of loci. We also discuss the effects of population bottlenecks on covariances among relatives.}, author = {Hill, William G and Nicholas Barton and Turelli, Michael}, journal = {Theoretical Population Biology}, number = {1}, pages = {56 -- 62}, publisher = {Academic Press}, title = {{Prediction of effects of genetic drift on variance components under a general model of epistasis}}, doi = {10.1016/j.tpb.2005.10.001}, volume = {70}, year = {2006}, } @inproceedings{3679, abstract = {This paper describes a new system for "Finding Satellite Tracks” in astronomical images based on the modern geometric approach. There is an increasing need of using methods with solid mathematical and statistical foundation in astronomical image processing. Where the computational methods are serving in all disciplines of science, they are becoming popular in the field of astronomy as well. Currently different computational systems are required to be numerically optimized before to get applied on astronomical images. So at present there is no single system which solves the problems of astronomers using computational methods based on modern approaches. The system "Finding Satellite Tracks” is based on geometric matching method "Recognition by Adaptive Subdivision of Transformation Space (RAST)".}, author = {Ali,Haider and Christoph Lampert and Breuel,Thomas M}, pages = {892 -- 901}, publisher = {Springer}, title = {{Satellite tracks removal in astronomical images}}, doi = {10.1007/11892755_92}, volume = {4225}, year = {2006}, } @inproceedings{3677, abstract = {We propose a video retrieval framework based on a novel combination of spatiograms and the Jensen-Shannon divergence, and validate its performance in two quantitative experiments on TRECVID BBC Rushes data. In the first experiment, color-based methods are tested by grouping redundant shots in an unsupervised clustering. Results of the second experiment show that motion-based spatiograms make a promising fast, compressed-domain descriptor for the detection of interview scenes.}, author = {Ulges, Adrian and Christoph Lampert and Keysers,Daniel}, pages = {1 -- 10}, publisher = {NIST (National Institute of Standards and Technology, US Department of Commerce)}, title = {{Spatiogram-based shot distances for video retrieval}}, year = {2006}, } @inproceedings{3680, abstract = {The detection of counterfeit in printed documents is currently based mainly on built-in security features or on human expertise. We propose a classification system that supports non-expert users to distinguish original documents from PC-made forgeries by analyzing the printing technique used. Each letter in a document is classified using a support vector machine that has been trained to distinguish laser from inkjet printouts. A color-coded visualization helps the user to interpret the per-letter classification results}, author = {Christoph Lampert and Mei,Lin and Breuel,Thomas M}, pages = {639 -- 634}, publisher = {IEEE}, title = {{Printing technique classification for document counterfeit detection}}, doi = {10.1109/ICCIAS.2006.294214}, volume = {1}, year = {2006}, } @article{3695, abstract = {We give an analytical and geometrical treatment of what it means to separate a Gaussian kernel along arbitrary axes in Ropfn, and we present a separation scheme that allows us to efficiently implement anisotropic Gaussian convolution filters for data of arbitrary dimensionality. Based on our previous analysis we show that this scheme is optimal with regard to the number of memory accesses and interpolation operations needed. The proposed method relies on nonorthogonal convolution axes and works completely in image space. Thus, it avoids the need for a fast Fourier transform (FFT)-subroutine. Depending on the accuracy and speed requirements, different interpolation schemes and methods to implement the one-dimensional Gaussian (finite impulse response and infinite impulse response) can be integrated. Special emphasis is put on analyzing the performance and accuracy of the new method. In particular, we show that without any special optimization of the source code, it can perform anisotropic Gaussian filtering faster than methods relying on the FFT.}, author = {Christoph Lampert and Wirjadi,Oliver}, journal = {IEEE Transactions on Image Processing (TIP)}, number = {11}, pages = {3501 -- 3513}, publisher = {IEEE}, title = {{An optimal non-orthogonal separation of the anisotropic Gaussian convolution filter}}, doi = { 10.1109/TIP.2006.877501 }, volume = {15}, year = {2006}, } @inproceedings{3693, abstract = {Gaussian filtering in one, two or three dimensions is among the most commonly needed tasks in signal and image processing. Finite impulse response filters in the time domain with Gaussian masks are easy to implement in either floating or fixed point arithmetic, because Gaussian kernels are strictly positive and bounded. But these implementations are slow for large images or kernels. With the recursive IIR-filters and FFT-based methods, there are at least two alternative methods to perform Gaussian filtering in a faster way, but so far they are only applicable when floating-point hardware is available. In this paper, a fixed-point implementation of recursive Gaussian filtering is discussed and applied to isotropic and anisotropic image filtering by making use of a non-orthogonal separation scheme of the Gaussian filter.}, author = {Christoph Lampert and Wirjadi,Oliver}, pages = {1565 -- 1568}, publisher = {IEEE}, title = {{Anisotropic Gaussian filtering using fixed point arithmetic}}, doi = {10.1109/ICIP.2006.312606}, year = {2006}, } @inproceedings{3692, author = {Keysers,Daniel and Christoph Lampert and Breuel,Thomas M}, publisher = {SPIE}, title = {{Color image dequantization by constrained diffusion}}, doi = {10.1117/12.648713}, volume = {6058}, year = {2006}, } @article{3729, abstract = {Measuring the visco-elastic properties of biological macromolecules constitutes an important step towards the understanding of dynamic biological processes, such as cell adhesion, muscle function, or plant cell wall stability. Force spectroscopy techniques based on the atomic force microscope (AFM) are increasingly used to study the complex visco-elastic response of (bio-)molecules on a single-molecule level. These experiments either require that the AFM cantilever is actively oscillated or that the molecule is clamped at constant force to monitor thermal cantilever motion. Here we demonstrate that the visco-elasticity of single bio-molecules can readily be extracted from the Brownian cantilever motion during conventional force-extension measurements. It is shown that the characteristics of the cantilever determine the signal-to-noise (S/N) ratio and time resolution. Using a small cantilever, the visco-elastic properties of single dextran molecules were resolved with a time resolution of 8.3 ms. The presented approach can be directly applied to probe the dynamic response of complex bio-molecular systems or proteins in force-extension experiments.}, author = {Bippes, Christian A and Humphris, Andrew D and Stark, Martin and Mueller, Daniel J and Harald Janovjak}, journal = {European Biophysics Journal}, number = {3}, pages = {287 -- 292}, publisher = {Springer}, title = {{Direct measurement of single-molecule visco-elasticity in atomic force microscope force-extension experiments}}, doi = {10.1007/s00249-005-0023-9}, volume = {35}, year = {2006}, } @article{3728, abstract = {Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard–Jones contact interactions is applied to model the protein–membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.}, author = {Cieplak, Marek and Filipek, Sławomir and Harald Janovjak and Krzysko, Krystiana A}, journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes}, number = {4}, pages = {537 -- 544}, publisher = {Elsevier}, title = {{Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment}}, doi = {10.1016/j.bbamem.2006.03.028}, volume = {1758}, year = {2006}, } @inbook{3722, author = {Harald Janovjak and Mueller, Daniel J}, booktitle = {Bioanalytik}, publisher = {Spektrum Akademischer Verlag}, title = {{Rastersondenmikroskopie}}, year = {2006}, } @article{3755, abstract = {A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems.}, author = {Le,Thuc T. and Emonet,Thierry and Harlepp, Sébastien and Calin Guet and Cluzel,Philippe}, journal = {Biophysical Journal}, number = {9}, pages = {3315 -- 3321}, publisher = {Biophysical Society}, title = {{Dynamical determinants of drug-inducible gene expression in a single bacterium}}, doi = {10.1529/biophysj.105.073353}, volume = {90}, year = {2006}, } @inproceedings{3758, abstract = {Control of physical simulation has become a popular topic in the field of computer graphics. Keyframe control has been applied to simulations of rigid bodies, smoke, liquid, flocks, and finite element-based elastic bodies. In this paper, we create a framework for controlling systems of interacting particles -- paying special attention to simulations of cloth and flocking behavior. We introduce a novel integrator-swapping approximation in order to apply the adjoint method to linearized implicit schemes appropriate for cloth simulation. This allows the control of cloth while avoiding computationally infeasible derivative calculations. Meanwhile, flocking control using the adjoint method is significantly more efficient than currently-used methods for constraining group behaviors, allowing the controlled simulation of greater numbers of agents in fewer optimization iterations.}, author = {Wojtan, Christopher J and Mucha, Peter and Turk, Greg}, pages = {15 -- 23}, publisher = {ACM}, title = {{Keyframe control of complex particle systems using the adjoint method}}, year = {2006}, } @article{3818, abstract = {Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein.}, author = {Bischofberger, Josef and Engel, Dominique and Li, Liyi and Geiger, Jörg R and Peter Jonas}, journal = {Nature Protocols}, number = {4}, pages = {2075 -- 81}, publisher = {Nature Publishing Group}, title = {{Patch-clamp recording from mossy fiber terminals in hippocampal slices}}, doi = {10.1038/nprot.2006.312 }, volume = {1}, year = {2006}, } @inproceedings{3890, abstract = {We consider two-player infinite games played on graphs. The games are concurrent, in that at each state the players choose their moves simultaneously and independently, and stochastic, in that the moves determine a probability distribution for the successor state. The value of a game is the maximal probability with which a player can guarantee the satisfaction of her objective. We show that the values of concurrent games with w-regular objectives expressed as parity conditions can be decided in NP boolean AND coNP. This result substantially improves the best known previous bound of 3EXPTIME. It also shows that the full class of concurrent parity games is no harder than the special case of turn-based stochastic reachability games, for which NP boolean AND coNP is the best known bound. While the previous, more restricted NP boolean AND coNP results for graph games relied on the existence of particularly simple (pure memoryless) optimal strategies, in concurrent games with parity objectives optimal strategies may not exist, and epsilon-optimal strategies (which achieve the value of the game within a parameter epsilon > 0) require in general both randomization and infinite memory. Hence our proof must rely on a more detailed analysis of strategies and, in addition to the main result, yields two results that are interesting on their own. First, we show that there exist epsilon-optimal strategies that in the limit coincide with memoryless strategies; this parallels the celebrated result of Mertens-Neyman for concurrent games with limit-average objectives. Second, we complete the characterization of the memory requirements for epsilon-optimal strategies for concurrent games with parity conditions, by showing that memoryless strategies suffice for epsilon-optimality for coBachi conditions.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger}, pages = {678 -- 687}, publisher = {SIAM}, title = {{The complexity of quantitative concurrent parity games}}, doi = {10.1145/1109557.1109631}, year = {2006}, } @inproceedings{3889, abstract = {We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds.}, author = {Krishnendu Chatterjee and Doyen, Laurent and Thomas Henzinger and Raskin, Jean-François}, pages = {287 -- 302}, publisher = {Springer}, title = {{Algorithms for omega-regular games with imperfect information}}, doi = {10.1007/11874683_19}, volume = {4207}, year = {2006}, } @inproceedings{3891, abstract = {We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).}, author = {Krishnendu Chatterjee}, pages = {256 -- 270}, publisher = {Springer}, title = {{Concurrent games with tail objectives}}, doi = {10.1007/11874683_17}, volume = {4207}, year = {2006}, } @inproceedings{3888, abstract = {A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with omega-regular winning conditions specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete, respectively. The value of the game for a player at a state s given an objective Phi is the maximal probability with which the player can guarantee the satisfaction of Phi from s. We present a strategy-improvement algorithm to compute values in stochastic Rabin games, where an improvement step involves solving Markov decision processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values for stochastic Streett games but does not directly yield an optimal strategy for Streett objectives. We then show how to obtain an optimal strategy for Streett objectives by solving certain nonstochastic Streett games.}, author = {Krishnendu Chatterjee and Thomas Henzinger}, pages = {375 -- 389}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Strategy improvement for stochastic Rabin and Streett games}}, doi = {10.1007/11817949_25}, volume = {4137}, year = {2006}, } @article{3908, abstract = {It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.}, author = {Ustinova, Jana and Achmann, Roland and Cremer, Sylvia and Mayer, Frieder}, journal = {Journal of Molecular Evolution}, number = {2}, pages = {158 -- 167}, publisher = {Springer}, title = {{Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus}}, doi = {10.1007/s00239-005-0022-6}, volume = {62}, year = {2006}, } @article{3934, abstract = {T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla.}, author = {Drumea-Mirancea, Mihaela and Wessels, Johannes T and Müller, Claudia A and Essl, Mike and Eble, Johannes A and Tolosa, Eva and Koch, Manuel and Reinhardt, Dieter P and Michael Sixt and Sorokin, Lydia and Stierhof, York-Dieter and Schwarz, Heinz and Klein, Gerd}, journal = {Journal of Cell Science}, number = {Pt 7}, pages = {1396 -- 1405}, publisher = {Company of Biologists}, title = {{Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules}}, doi = {10.1242/​jcs.02840}, volume = {119}, year = {2006}, } @article{3935, abstract = {Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis.}, author = {Chu, Haiyan and Thievessen, Ingo and Michael Sixt and Lämmermann, Tim and Waisman, Ari and Braun, Attila and Noegel, Angelika A and Fässler, Reinhard}, journal = {Molecular and Cellular Biology}, number = {5}, pages = {1817 -- 1825}, publisher = {American Society for Microbiology}, title = {{γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response}}, doi = {10.1128/MCB.26.5.1817-1825.2006}, volume = {26}, year = {2006}, } @article{3936, abstract = {At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials.}, author = {Michael Sixt and Bauer, Martina and Lämmermann, Tim and Fässler, Reinhard}, journal = {Current Opinion in Cell Biology}, number = {5}, pages = {482 -- 490}, publisher = {Elsevier}, title = {{β1 integrins: zip codes and signaling relay for blood cells}}, doi = {10.1016/j.ceb.2006.08.007}, volume = {18}, year = {2006}, } @article{4140, abstract = {Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation.}, author = {Witzel, Sabine and Zimyanin, Vitaly and Carreira Barbosa, Filipa and Tada, Masazumi and Heisenberg, Carl-Philipp J}, journal = {Journal of Cell Biology}, number = {5}, pages = {791 -- 802}, publisher = {Rockefeller University Press}, title = {{Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane}}, doi = {10.1083/jcb.200606017}, volume = {175}, year = {2006}, } @article{4145, abstract = {The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development.}, author = {Tonelli, Davide and Calegari, Frederico and Fei, Ji and Nomura, Tadashi and Osumi, Noriko and Heisenberg, Carl-Philipp J and Huttner, Wieland}, journal = {Biotechniques}, number = {6}, pages = {727 -- 732}, publisher = {Informa Healthcare}, title = {{Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid}}, doi = {10.2144/000112296}, volume = {41}, year = {2006}, } @article{4176, abstract = {During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development.}, author = {Link, Vinzenz and Carvalho, Lara and Castanon, Irinka and Stockinger, Petra and Shevchenko, Andrej and Heisenberg, Carl-Philipp J}, journal = {Journal of Cell Science}, number = {10}, pages = {2073 -- 2083}, publisher = {Company of Biologists}, title = {{Identification of regulators of germ layer morphogenesis using proteomics in zebrafish}}, doi = {10.1242/jcs.02928}, volume = {119}, year = {2006}, } @article{4173, abstract = {Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.}, author = {Link, Vinzenz and Shevchenko, Andrej and Heisenberg, Carl-Philipp J}, journal = {BMC Developmental Biology}, pages = {1 -- 9}, publisher = {BioMed Central}, title = {{Proteomics of early zebrafish embryos}}, doi = {10.1186/1471-213X-6-1}, volume = {6}, year = {2006}, } @article{4178, abstract = {Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools.}, author = {Langenberg, Tobias and Dracz, Tadeusz and Oates, Andrew and Heisenberg, Carl-Philipp J and Brand, Michael}, journal = {Developmental Dynamics}, number = {4}, pages = {928 -- 933}, publisher = {Wiley-Blackwell}, title = {{Analysis and visualization of cell movement in the developing zebrafish brain}}, doi = {10.1002/dvdy.20692}, volume = {235}, year = {2006}, } @article{4184, abstract = {Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis.}, author = {Köppen, Mathias and Fernández, Beatriz and Carvalho, Lara and Jacinto, António and Heisenberg, Carl-Philipp J}, journal = {Development}, number = {14}, pages = {2671 -- 2681}, publisher = {Company of Biologists}, title = {{Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila}}, doi = {doi: 10.1242/dev.02439}, volume = {133}, year = {2006}, } @article{4218, abstract = {The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration.}, author = {Blaser, Heiko and Reichman Fried, Michal and Castanon, Irinka and Dumstrei, Karin and Marlow, Florence and Kawakami, Koichi and Solnica Krezel, Lilianna and Heisenberg, Carl-Philipp J and Raz, Erez}, journal = {Developmental Cell}, number = {5}, pages = {613 -- 627}, publisher = {Cell Press}, title = {{Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow}}, doi = {10.1016/j.devcel.2006.09.023}, volume = {11}, year = {2006}, }