@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}, }