@article{9457, abstract = {Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.}, author = {Zilberman, Daniel and Coleman-Derr, Devin and Ballinger, Tracy and Henikoff, Steven}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7218}, pages = {125--129}, publisher = {Springer Nature}, title = {{Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks}}, doi = {10.1038/nature07324}, volume = {456}, year = {2008}, } @article{9537, abstract = {DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more.}, author = {Zilberman, Daniel}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, number = {5}, pages = {554--559}, publisher = {Elsevier }, title = {{The evolving functions of DNA methylation}}, doi = {10.1016/j.pbi.2008.07.004}, volume = {11}, year = {2008}, } @article{965, abstract = {We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.}, author = {Morozov, Alexei Y and Maksym Serbyn}, journal = {Theoretical and Mathematical Physics}, number = {2}, pages = {270 -- 293}, publisher = {Elsevier}, title = {{Nonlinear algebra and Bogoliubov's recursion}}, doi = {10.1007/s11232-008-0026-7}, volume = {154}, year = {2008}, } @article{11109, abstract = {The nuclear envelope (NE) provides a selective barrier between the nuclear interior and the cytoplasm and constitutes a central component of intracellular architecture. During mitosis in metazoa, the NE breaks down leading to the complete mixing of the nuclear content with the cytosol. Interestingly, many NE components actively participate in mitotic progression. After chromosome segregation, the NE is reassembled around decondensing chromatin and the nuclear compartment is reestablished in the daughter cells. Here, we summarize recent progress in deciphering the molecular mechanisms underlying NE dynamics during cell division.}, author = {Kutay, Ulrike and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {6}, pages = {669--677}, publisher = {Elsevier}, title = {{Reorganization of the nuclear envelope during open mitosis}}, doi = {10.1016/j.ceb.2008.09.010}, volume = {20}, year = {2008}, } @article{11110, abstract = {Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, thereby connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures, the only function of which was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we discuss the most recent developments in the nuclear-pore-complex field, focusing on the assembly, disassembly, maintenance and function of this macromolecular structure.}, author = {D’Angelo, Maximiliano A. and HETZER, Martin W}, issn = {0962-8924}, journal = {Trends in Cell Biology}, keywords = {Cell Biology}, number = {10}, pages = {456--466}, publisher = {Elsevier}, title = {{Structure, dynamics and function of nuclear pore complexes}}, doi = {10.1016/j.tcb.2008.07.009}, volume = {18}, year = {2008}, } @article{11111, abstract = {During mitosis in metazoans, segregated chromosomes become enclosed by the nuclear envelope (NE), a double membrane that is continuous with the endoplasmic reticulum (ER). Recent in vitro data suggest that NE formation occurs by chromatin-mediated reorganization of the tubular ER; however, the basic principles of such a membrane-reshaping process remain uncharacterized. Here, we present a quantitative analysis of nuclear membrane assembly in mammalian cells using time-lapse microscopy. From the initial recruitment of ER tubules to chromatin, the formation of a membrane-enclosed, transport-competent nucleus occurs within ∼12 min. Overexpression of the ER tubule-forming proteins reticulon 3, reticulon 4, and DP1 inhibits NE formation and nuclear expansion, whereas their knockdown accelerates nuclear assembly. This suggests that the transition from membrane tubules to sheets is rate-limiting for nuclear assembly. Our results provide evidence that ER-shaping proteins are directly involved in the reconstruction of the nuclear compartment and that morphological restructuring of the ER is the principal mechanism of NE formation in vivo.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {5}, pages = {911--924}, publisher = {Rockefeller University Press}, title = {{Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation}}, doi = {10.1083/jcb.200805140}, volume = {182}, year = {2008}, } @article{11112, abstract = {The nuclear envelope is a double-layered membrane that encloses the nuclear genome and transcriptional machinery. In dividing cells of metazoa, the nucleus completely disassembles during mitosis, creating the need to re-establish the nuclear compartment at the end of each cell division. Given the crucial role of the nuclear envelope in gene regulation and cellular organization, it is not surprising that its biogenesis and organization have become active research areas. We will review recent insights into nuclear membrane dynamics during the cell cycle.}, author = {Anderson, Daniel J and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {4}, pages = {386--392}, publisher = {Elsevier}, title = {{The life cycle of the metazoan nuclear envelope}}, doi = {10.1016/j.ceb.2008.03.016}, volume = {20}, year = {2008}, } @article{11113, abstract = {The nuclear envelope (NE), a double membrane enclosing the nucleus of eukaryotic cells, controls the flow of information between the nucleoplasm and the cytoplasm and provides a scaffold for the organization of chromatin and the cytoskeleton. In dividing metazoan cells, the NE breaks down at the onset of mitosis and then reforms around segregated chromosomes to generate the daughter nuclei. Recent data from intact cells and cell-free nuclear assembly systems suggest that the endoplasmic reticulum (ER) is the source of membrane for NE assembly. At the end of mitosis, ER membrane tubules are targeted to chromatin via tubule ends and reorganized into flat nuclear membrane sheets by specific DNA-binding membrane proteins. In contrast to previous models, which proposed vesicle fusion to be the principal mechanism of NE formation, these new studies suggest that the nuclear membrane forms by the chromatin-mediated reshaping of the ER.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1477-9137}, journal = {Journal of Cell Science}, keywords = {Cell Biology}, number = {2}, pages = {137--142}, publisher = {The Company of Biologists}, title = {{Shaping the endoplasmic reticulum into the nuclear envelope}}, doi = {10.1242/jcs.005777}, volume = {121}, year = {2008}, } @article{11114, abstract = {We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment.}, author = {Schulte, Roberta and Talamas, Jessica and Doucet, Christine and HETZER, Martin W}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions}}, doi = {10.1371/journal.pone.0002061}, volume = {3}, year = {2008}, } @article{11878, abstract = {Given only the URL of a web page, can we identify its language? This is the question that we examine in this paper. Such a language classifier is, for example, useful for crawlers of web search engines, which frequently try to satisfy certain language quotas. To determine the language of uncrawled web pages, they have to download the page, which might be wasteful, if the page is not in the desired language. With URL-based language classifiers these redundant downloads can be avoided. We apply a variety of machine learning algorithms to the language identification task and evaluate their performance in extensive experiments for five languages: English, French, German, Spanish and Italian. Our best methods achieve an F-measure, averaged over all languages, of around .90 for both a random sample of 1,260 web page from a large web crawl and for 25k pages from the ODP directory. For 5k pages of web search engine results we even achieve an F-measure of .96. The achieved recall for these collections is .93, .88 and .95 respectively. Two independent human evaluators performed considerably worse on the task, with an F-measure of .75 and a typical recall of a mere .67. Using only country-code top-level domains, such as .de or .fr yields a good precision, but a typical recall of below .60 and an F-measure of around .68.}, author = {Baykan, Eda and Henzinger, Monika H and Weber, Ingmar}, issn = {2150-8097}, journal = {Proceedings of the VLDB Endowment}, number = {1}, pages = {176--187}, publisher = {Association for Computing Machinery}, title = {{Web page language identification based on URLs}}, doi = {10.14778/1453856.1453880}, volume = {1}, year = {2008}, } @inproceedings{2078, abstract = {This paper presents a novel method for real-time animation of highly-detailed facial expressions based on a multi-scale decomposition of facial geometry into large-scale motion and fine-scale details, such as expression wrinkles. Our hybrid animation is tailored to the specific characteristics of large- and fine-scale facial deformations: Large-scale deformations are computed with a fast linear shell model, which is intuitively and accurately controlled through a sparse set of motion-capture markers or user-defined handle points. Fine-scale facial details are incorporated using a novel pose-space deformation technique, which learns the correspondence of sparse measurements of skin strain to wrinkle formation from a small set of example poses. Our hybrid method features real-time animation of highly-detailed faces with realistic wrinkle formation, and allows both large-scale deformations and fine-scale wrinkles to be edited intuitively. Furthermore, our pose-space representation enables the transfer of facial details to novel expressions or other facial models.}, author = {Bickel, Bernd and Lang, Manuel and Botsch, Mario and Otaduy, Miguel and Gross, Markus}, pages = {57 -- 66}, publisher = {ACM}, title = {{Pose-space animation and transfer of facial details}}, doi = {10.2312/SCA/SCA08/057-066}, year = {2008}, } @article{2120, abstract = {We consider the linear stochastic Cauchy problem dX (t) =AX (t) dt +B dWH (t), t≥ 0, where A generates a C0-semigroup on a Banach space E, WH is a cylindrical Brownian motion over a Hilbert space H, and B: H → E is a bounded operator. Assuming the existence of a unique minimal invariant measure μ∞, let Lp denote the realization of the Ornstein-Uhlenbeck operator associated with this problem in Lp (E, μ∞). Under suitable assumptions concerning the invariance of the range of B under the semigroup generated by A, we prove the following domain inclusions, valid for 1 < p ≤ 2: Image omitted. Here WHk, p (E, μinfin; denotes the kth order Sobolev space of functions with Fréchet derivatives up to order k in the direction of H. No symmetry assumptions are made on L p.}, author = {Jan Maas and van Neerven, Jan M}, journal = {Infinite Dimensional Analysis, Quantum Probability and Related Topics}, number = {4}, pages = {603 -- 626}, publisher = {World Scientific Publishing}, title = {{On the domain of non-symmetric Ornstein-Uhlenbeck operators in banach spaces}}, doi = {10.1142/S0219025708003245}, volume = {11}, year = {2008}, } @article{2121, abstract = {Let H be a separable real Hubert space and let double struck F sign = (ℱt)t∈[0,T] be the augmented filtration generated by an H-cylindrical Brownian motion (WH(t))t∈[0,T] on a probability space (Ω, ℱ ℙ). We prove that if E is a UMD Banach space, 1 ≤ p < ∞, and F ∈ double struck D sign1,p(Ω E) is ℱT-measurable, then F = double struck E sign(F) + ∫0T Pdouble struck F sign(DF) dW H, where D is the Malliavin derivative of F and P double struck F sign is the projection onto the F-adapted elements in a suitable Banach space of Lp-stochastically integrable ℒ(H, E)-valued processes.}, author = {van Neerven, Jan M and Jan Maas}, journal = {Electronic Communications in Probability}, pages = {151 -- 164}, publisher = {Institute of Mathematical Statistics}, title = {{A Clark-Ocone formula in UMD Banach spaces}}, volume = {13}, year = {2008}, } @article{2146, abstract = {We present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the “shape” of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne–OCS(Σ1) and Ar–NO(Π2) systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett.313, 491 (1999)] demonstrates the model’s ability to qualitatively explain the field dependence of all the scattering features observed.}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, journal = {Journal of Chemical Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{An analytic model of rotationally inelastic collisions of polar molecules in electric fields}}, doi = {10.1063/1.2948392}, volume = {129}, year = {2008}, } @misc{2147, abstract = {We present the physics of the quantum Zeno effect, whose gist is often expressed by invoking the adage "a watched pot never boils". We review aspects of the theoretical and experimental work done on the effect since its inception in 1977, and mention some applications. We dedicate the article - with our very best wishes - to Rudolf Zahradnik at the occasion of his great jubilee. Perhaps Rudolf's lasting youthfulness and freshness are due to that he himself had been frequently observed throughout his life: until the political turn-around in 1989 by those who wished, by their surveillance, to prevent Rudolf from spoiling the youth by his personal culture and his passion for science and things beautiful and useful in general. This attempt had failed. Out of gratitude, the youth has infected Rudolf with its youthfulness. Chronically. Since 1989, Rudolf has been closely watched by the public at large. For the same traits of his as before, but with the opposite goal and for the benefit of all generations. We relish keeping him in sight...}, author = {Mikhail Lemeshko and Friedrich, Břetislav}, booktitle = {Chemicke Listy}, number = {10}, pages = {880 -- 883}, publisher = {Czech Society of Chemical Engineering}, title = {{Kvantový Zenonův jev aneb co nesejde z očí, nezestárne}}, volume = {102}, year = {2008}, } @article{2148, abstract = {Despite the growing geological evidence that fluid boiling and vapour-liquid separation affect the distribution of metals in magmatic-hydrothermal systems significantly, there are few experimental data on the chemical status and partitioning of metals in the vapour and liquid phases. Here we report on an in situ measurement, using X-ray absorption fine structure (XAFS) spectroscopy, of antimony speciation and partitioning in the system Sb2O3-H2O-NaCl-HCl at 400°C and pressures 270–300 bar corresponding to the vapour-liquid equilibrium. Experiments were performed using a spectroscopic cell which allows simultaneous determination of the total concentration and atomic environment of the absorbing element (Sb) in each phase. Results show that quantitative vapour-brine separation of a supercritical aqueous salt fluid can be achieved by a controlled decompression and monitoring the X-ray absorbance of the fluid phase. Antimony concentrations in equilibrium with Sb2O3 (cubic, senarmontite) in the coexisting vapour and liquid phases and corresponding SbIII vapour-liquid partitioning coefficients are in agreement with recent data obtained using batch-reactor solubility techniques. The XAFS spectra analysis shows that hydroxy-chloride complexes, probably Sb(OH)2Cl0, are dominant both in the vapour and liquid phase in a salt-water system at acidic conditions. This first in situ XAFS study of element fractionation between coexisting volatile and dense phases opens new possibilities for systematic investigations of vapour-brine and fluid-melt immiscibility phenomena, avoiding many experimental artifacts common in less direct techniques.}, author = {Pokrovski, Gleb S and Roux, Jacques L and Hazemann, Jean L and Borisova, Anastassia Y and Gonchar, Anastasia A and Mikhail Lemeshko}, journal = {Mineralogical Magazine}, number = {2}, pages = {667 -- 681}, publisher = {Mineralogical Society}, title = {{In situ X-ray absorption spectroscopy measurement of vapour-brine fractionation of antimony at hydrothermal conditions}}, doi = {10.1180/minmag.2008.072.2.667 }, volume = {72}, year = {2008}, } @article{224, abstract = {Let n ≥ 4 and let Q ∈ [X1, ..., Xn] be a non-singular quadratic form. When Q is indefinite we provide new upper bounds for the least non-trivial integral solution to the equation Q = 0, and when Q is positive definite we provide improved upper bounds for the greatest positive integer k for which the equation Q = k is insoluble in integers, despite being soluble modulo every prime power.}, author = {Timothy Browning and Dietmann, Rainer}, journal = {Proceedings of the London Mathematical Society}, number = {2}, pages = {389 -- 416}, publisher = {John Wiley and Sons Ltd}, title = {{On the representation of integers by quadratic forms}}, doi = {10.1112/plms/pdm032}, volume = {96}, year = {2008}, } @article{225, abstract = {We revisit recent work of Heath-Brown on the average order of the quantity r(L1(x))⋯r(L4(x)), for suitable binary linear forms L1,...,L4, as x=(x1,x2) ranges over quite general regions in ℤ2. In addition to improving the error term in Heath-Browns estimate, we generalise his result to cover a wider class of linear forms.}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Compositio Mathematica}, number = {6}, pages = {1375 -- 1402}, publisher = {Cambridge University Press}, title = {{Binary linear forms as sums of two squares}}, doi = {10.1112/S0010437X08003692}, volume = {144}, year = {2008}, } @inproceedings{2331, abstract = {We present a review of recent work on the mathematical aspects of the BCS gap equation, covering our results of Ref. 9 as well our recent joint work with Hamza and Solovej and with Frank and Naboko, respectively. In addition, we mention some related new results.}, author = {Hainzl, Christian and Robert Seiringer}, pages = {117 -- 136}, publisher = {World Scientific Publishing}, title = {{ Spectral properties of the BCS gap equation of superfluidity}}, doi = {10.1142/9789812832382_0009}, year = {2008}, } @inproceedings{2332, abstract = {We present a rigorous proof of the appearance of quantized vortices in dilute trapped Bose gases with repulsive two-body interactions subject to rotation, which was obtained recently in joint work with Elliott Lieb.14 Starting from the many-body Schrödinger equation, we show that the ground state of such gases is, in a suitable limit, well described by the nonlinear Gross-Pitaevskii equation. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.}, author = {Robert Seiringer}, pages = {241 -- 254}, publisher = {World Scientific Publishing}, title = {{Vortices and Spontaneous Symmetry Breaking in Rotating Bose Gases}}, doi = {10.1142/9789812832382_0017}, year = {2008}, }