TY - JOUR AB - The nuclear envelope (NE) is a highly specialized membrane that delineates the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates the trafficking of macromolecules between nucleoplasm and cytosol but also provides anchoring sites for chromatin and the cytoskeleton. Through these interactions, the NE helps position the nucleus within the cell and chromosomes within the nucleus, thereby regulating the expression of certain genes. The NE is not static, rather it is continuously remodeled during cell division. The most dramatic example of NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic cell life, relatively little is known about its biogenesis or many of its functions. We thus are far from understanding the molecular etiology of a diverse group of NE-associated diseases. AU - HETZER, Martin W AU - Walther, Tobias C. AU - Mattaj, Iain W. ID - 11120 JF - Annual Review of Cell and Developmental Biology KW - Cell Biology KW - Developmental Biology SN - 1081-0706 TI - Pushing the envelope: Structure, function, and dynamics of the nuclear periphery VL - 21 ER - TY - CONF AB - We give a short survey of the use of hyperlink analysis in web search engine ranking and sketch other applications of hyperlink analysis in the web space. AU - Henzinger, Monika H ID - 11698 KW - Hyperlink Analysis KW - World Wide Web SN - 9781595931689 T2 - Proceedings of the 16th ACM conference on Hypertext and hypermedia TI - Hyperlink analysis on the world wide web ER - TY - JOUR AB - Many daily activities present information in the form of a stream of text, and often people can benefit from additional information on the topic discussed. TV broadcast news can be treated as one such stream of text; in this paper we discuss finding news articles on the web that are relevant to news currently being broadcast. We evaluated a variety of algorithms for this problem, looking at the impact of inverse document frequency, stemming, compounds, history, and query length on the relevance and coverage of news articles returned in real time during a broadcast. We also evaluated several postprocessing techniques for improving the precision, including reranking using additional terms, reranking by document similarity, and filtering on document similarity. For the best algorithm, 84–91% of the articles found were relevant, with at least 64% of the articles being on the exact topic of the broadcast. In addition, a relevant article was found for at least 70% of the topics. AU - Henzinger, Monika H AU - Chang, Bay-Wei AU - Milch, Brian AU - Brin, Sergey ID - 11904 IS - 2 JF - World Wide Web SN - 1386-145X TI - Query-free news search VL - 8 ER - TY - JOUR AB - We present the first polylog-competitive online algorithm for the general multicast admission control and routing problem in the throughput model. The ratio of the number of requests accepted by the optimum offline algorithm to the expected number of requests accepted by our algorithm is O((log n + log log M)(log n + log M) log n), where M is the number of multicast groups and n is the number of nodes in the graph. We show that this is close to optimum by presenting an Ω(log n log M) lower bound on this ratio for any randomized online algorithm against an oblivious adversary, when M is much larger than the link capacities. Our lower bound applies even in the restricted case where the link capacities are much larger than bandwidth requested by a single multicast. We also present a simple proof showing that it is impossible to be competitive against an adaptive online adversary. As in the previous online routing algorithms, our algorithm uses edge-costs when deciding on which is the best path to use. In contrast to the previous competitive algorithms in the throughput model, our cost is not a direct function of the edge load. The new cost definition allows us to decouple the effects of routing and admission decisions of different multicast groups. AU - Goel, Ashish AU - Henzinger, Monika H AU - Plotkin, Serge ID - 11763 IS - 1 JF - Journal of Algorithms SN - 0196-6774 TI - An online throughput-competitive algorithm for multicast routing and admission control VL - 55 ER - TY - JOUR AB - An enhanced temperature-index glacier melt model, incorporating incoming shortwave radiation and albedo, is presented. The model is an attempt to combine the high temporal resolution and accuracy of physically based melt models with the lower data requirements and computational simplicity of empirical melt models, represented by the ‘degree-day’ method and its variants. The model is run with both measured and modelled radiation data, to test its applicability to glaciers with differing data availability. Five automatic weather stations were established on Haut Glacier d’Arolla, Switzerland, between May and September 2001. Reference surface melt rates were calculated using a physically based energy-balance melt model. The performance of the enhanced temperature-index model was tested at each of the four validation stations by comparing predicted hourly melt rates with reference melt rates. Predictions made with three other temperature-index models were evaluated in the same way for comparison. The enhanced temperature-index model offers significant improvements over the other temperature-index models, and accounts for 90–95% of the variation in the reference melt rate. The improvement is lower, but still significant, when the model is forced by modelled shortwave radiation data, thus offering a better alternative to existing models that require only temperature data input. AU - Pellicciotti, Francesca AU - Brock, Ben AU - Strasser, Ulrich AU - Burlando, Paolo AU - Funk, Martin AU - Corripio, Javier ID - 12657 IS - 175 JF - Journal of Glaciology SN - 0022-1430 TI - An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland VL - 51 ER - TY - JOUR AB - Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals. AU - Reiff, Dierk F AU - Ihring, Alexandra AU - Guerrero, Giovanna AU - Isacoff, Ehud Y AU - Maximilian Jösch AU - Nakai, Junichi AU - Borst, Alexander ID - 1298 IS - 19 JF - Journal of Neuroscience TI - In vivo performance of genetically encoded indicators of neural activity in flies VL - 25 ER - TY - JOUR AB - Building on a recent paper [8], here we argue that the combinatorics of matroids are intimately related to the geometry and topology of toric hyperkähler varieties. We show that just like toric varieties occupy a central role in Stanley’s proof for the necessity of McMullen’s conjecture (or g-inequalities) about the classification of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties leads to new restrictions on face vectors of matroid complexes. Namely in this paper we will give two proofs that the injectivity part of the Hard Lefschetz theorem survives for toric hyperkähler varieties. We explain how this implies the g-inequalities for rationally representable matroids. We show how the geometrical intuition in the first proof, coupled with results of Chari [3], leads to a proof of the g-inequalities for general matroid complexes, which is a recent result of Swartz [20]. The geometrical idea in the second proof will show that a pure O-sequence should satisfy the g-inequalities, thus showing that our result is in fact a consequence of a long-standing conjecture of Stanley. AU - Tamas Hausel ID - 1447 IS - 1 JF - Open Mathematics TI - Quaternionic geometry of matroids VL - 3 ER - TY - CHAP AB - The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat connections and character varieties for curves, respectively. Several new results and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman and Earl-Kirwan are explained. These use the representation theory of finite groups of Lie-type via the arithmetic of character varieties and lead to an unexpected conjecture for a Hard Lefschetz theorem for their cohomology. AU - Tamas Hausel ID - 1444 T2 - Geometric Methods in Algebra and Number Theory TI - Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve VL - 235 ER - TY - JOUR AB - We study an integration theory in circle equivariant cohomology in order to prove a theorem relating the cohomology ring of a hyperkähler quotient to the cohomology ring of the quotient by a maximal abelian subgroup, analogous to a theorem of Martin for symplectic quotients. We discuss applications of this theorem to quiver varieties, and compute as an example the ordinary and equivariant cohomology rings of a hyperpolygon space. AU - Tamas Hausel AU - Proudfoot, Nicholas J ID - 1463 IS - 1 JF - Topology TI - Abelianization for hyperkähler quotients VL - 44 ER - TY - JOUR AB - The effects of substrate temperature, growth rate, and postgrowth annealing on the composition of Ge islands grown on Si(001) were investigated with a combination of selective wet chemical etching and atomic force microscopy. A simple kinetic model comprising only surface diffusion processes can explain all the experimentally observed compositional profiles for pyramid and dome islands grown in the 560-620°C range. From this model three-dimensional compositional maps were extracted. By performing annealing experiments a change in the composition of the domes was observed. This could be explained as the result of the islands' movement induced by alloying-driven energy minimization. Also in this case kinetically hindered bulk diffusion processes are not needed to explain the experimental observations. AU - Georgios Katsaros AU - Costantini, Giovanni AU - Stoffel, Mathieu AU - Esteban, Rubén AU - Bittner, Alexander M AU - Rastelli, Armando AU - Denker, Ulrich AU - Schmidt, Oliver G AU - Kern, Klaus ID - 1742 IS - 19 JF - Physical Review B - Condensed Matter and Materials Physics TI - Kinetic origin of island intermixing during the growth of Ge on Si (001) VL - 72 ER - TY - JOUR AB - A systematic study of the morphology of self-organized islands in the InAs/GaAs(0 0 1) and Ge/Si(0 0 1) systems is presented, based on high-resolution scanning tunneling microscopy measurements. We demonstrate that in both cases two main island families coexist: smaller pyramids bound by one type of shallow facets and larger multifaceted domes. Their structure and facet orientation are precisely determined, thus solving a highly debated argument in the case of InAs/GaAs(0 0 1). The comparison between the two material systems reveals the existence of striking similarities that extend even to the nature of island precursors and to the islands that form when depositing InGaAs or GeSi alloys. The implications of these observations on a possible universal description of the Stranski-Krastanow growth mode are discussed with respect to recent theoretical results. AU - Costantini, Giovanni AU - Rastelli, Armando AU - Manzano, Carlos AU - Acosta-Diaz, P AU - Georgios Katsaros AU - Songmuang, Rudeeson AU - Schmidt, Oliver G AU - Von Känel, Hans AU - Kern, Klaus ID - 1740 IS - 1-4 JF - Journal of Crystal Growth TI - Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems VL - 278 ER - TY - JOUR AB - Laterally aligned multilayer GeSiSi islands grown on a patterned Si (001) substrate are disclosed by selective etching of Si in a KOH solution. This procedure allows us to visualize the vertical alignment of the islands in a three-dimensional perspective. Our technique reveals that partly coalesced double islands in the initial layer do not merge together, but instead gradually reproduce into well-separated double islands in upper layers. We attribute this effect to very thin spacer layers, which efficiently transfer the strain modulation of each island through the spacer layer to the surface. The etching rate of Si is reduced in tensile strained regions, which helps to preserve sufficient Si between the stacked islands to form a periodic array of freestanding and vertically modulated heterostructure pillars. AU - Zhong, Zheyang AU - Georgios Katsaros AU - Stoffel, Mathieu AU - Costantini, Giovanni AU - Kern, Klaus AU - Schmidt, Oliver G AU - Jin-Phillipp, Neng Y AU - Bauer, Günther ID - 1743 IS - 26 JF - Applied Physics Letters TI - Periodic pillar structures by Si etching of multilayer GeSi/Si islands VL - 87 ER - TY - JOUR AB - This paper presents optical duobinary and dicode signalling, as alternatives to the binary format, in order to improve the transmission performance in the presense of non-linear effects in a dense wavelength division multiplex (WDM) optical system. Duobinary signalling is applied to an optical system to explore the reduction of stimulated Brillouin scattering (SBS) effects. Duobinary signalling suppresses the SBS effects, and an eye-opening improvement of 0.25 to 1.2 dB is achieved relative to binary transmission over a range of input power levels. An experimental study demonstrates that duobinary modulation suppresses the four wave mixing (FWM) products of a dense WDM system by a maximum of 3 dB. The suppression is maintained over a range of channel spacings. An investigation of the impact of fibre dispersion on FWM products under binary, duobinary and dicode modulation in a dense WDM system is then performed, with interchannel spacing and optical power variation. This leads to the development of a set of guidelines for the application areas, in which it is appropriate to use duobinary or dicode modulation in WDM systems as a means of mitigating the impact of FWM. AU - Georgios Katsaros AU - Darwazeh, Izzat Z AU - Lane, Phil M ID - 1744 IS - 6 JF - IEE Proceedings - Optoelectronics TI - Non linear transmission effects in duobinary and dicode optical systems VL - 152 ER - TY - JOUR AB - SiGe islands move laterally on a Si(001) substrate during in situ postgrowth annealing. This surprising behavior is revealed by an analysis of the substrate surface morphology after island removal using wet chemical etching. We explain the island motion by asymmetric surface-mediated alloying. Material leaves one side of the island by surface diffusion, and mixes with additional Si from the surrounding surface as it redeposits on the other side. Thus the island moves laterally while becoming larger and more dilute. AU - Denker, Ulrich AU - Rastelli, Armando AU - Stoffel, Mathieu AU - Tersoff, Jerry AU - Georgios Katsaros AU - Costantini, Giovanni AU - Kern, Klaus AU - Jin-Phillipp, Neng Y AU - Jesson, David E AU - Schmidt, Oliver G ID - 1741 IS - 21 JF - Physical Review Letters TI - Lateral motion of SiGe islands driven by surface-mediated alloying VL - 94 ER - TY - JOUR AB - Background: Murine leukemia virus (MLV) vector particles can be pseudotyped with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) and selectively target gene transfer to human cells expressing both CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY cells, which express the MLV gag and pol genes, we generated stable producer cell lines that express the HIV-1 envelope gene and a retroviral vector genome encoding the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed from a bicistronic vector which allowed the rapid selection of stable cell lines. A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env expression. Vectors generated by these producer cells displayed different sensitivity to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors are a valuable screening system for entry inhibitors or neutralizing antisera generated by vaccines. AU - Sandra Siegert AU - Thaler, Sonja AU - Wagner, Ralf AU - Schnierle, Barbara S ID - 1795 IS - 1 JF - AIDS Research and Therapy TI - Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors VL - 2 ER - TY - JOUR AB - Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I. AU - Hinchliffe, Philip AU - Leonid Sazanov ID - 1962 IS - 5735 JF - Science TI - Biochemistry: Organization of iron-sulfur clusters in respiratory complex I VL - 309 ER - TY - BOOK AB - Harold Davenport was one of the truly great mathematicians of the twentieth century. Based on lectures he gave at the University of Michigan in the early 1960s, this book is concerned with the use of analytic methods in the study of integer solutions to Diophantine equations and Diophantine inequalities. It provides an excellent introduction to a timeless area of number theory that is still as widely researched today as it was when the book originally appeared. The three main themes of the book are Waring's problem and the representation of integers by diagonal forms, the solubility in integers of systems of forms in many variables, and the solubility in integers of diagonal inequalities. For the second edition of the book a comprehensive foreword has been added in which three prominent authorities describe the modern context and recent developments. A thorough bibliography has also been added. AU - Davenport, Harold AU - Browning, Timothy D ID - 210 TI - Analytic Methods for Diophantine Equations and Diophantine Inequalities ER - TY - JOUR AB - Let f ∈ ℤ[x] be a polynomial of degree d. The paucity of non-trivial positive integer solutions to the equation f(x1)+f(x 2)=f(x3)+f(x4) is established, provided that d ≤ 7$. Also the corresponding situation is investigated for equal sums of three like polynomials. AU - Timothy Browning ID - 211 IS - 6 JF - Bulletin of the London Mathematical Society TI - Equal sums of like polynomials VL - 37 ER - TY - JOUR AB - For any n ≧ 2, let F ∈ ℤ [ x 1, … , xn ] be a form of degree d≧ 2, which produces a geometrically irreducible hypersurface in ℙn–1. This paper is concerned with the number N(F;B) of rational points on F = 0 which have height at most B. For any ε > 0 we establish the estimate N(F; B) = O(B n− 2+ ε ), whenever either n ≦ 5 or the hypersurface is not a union of lines. Here the implied constant depends at most upon d, n and ε. AU - Timothy Browning AU - Heath-Brown, Roger ID - 212 IS - 584 JF - Journal fur die Reine und Angewandte Mathematik TI - Counting rational points on hypersurfaces ER - TY - JOUR AB - Given an absolutely irreducible ternary form F, the purpose of this paper is to produce better upper bounds for the number of integer solutions to the equation F=0, that are restricted to lie in very lopsided boxes. As an application of the main result, a new paucity estimate is obtained for equal sums of two like powers. AU - Timothy Browning AU - Heath-Brown, Roger ID - 214 IS - 2 JF - Mathematische Zeitschrift TI - Plane curves in boxes and equal sums of two powers VL - 251 ER -