@article{877, abstract = {Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions producing pathogenic effects in humans are often found in normal, healthy individuals from other species. Analysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic mutations can be neutralized by other, compensatory substitutions that restore the structural stability of the molecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis- eases that may be based on the correction of molecule stability as a whole instead of reversing an individual pathogenic mutation.}, author = {Kondrashov, Fyodor}, journal = {Biofizika}, number = {3}, pages = {389 -- 395}, publisher = {Pleiades Publishing}, title = {{The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution}}, volume = {50}, year = {2005}, } @article{878, abstract = {Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions. }, author = {Fyodor Kondrashov}, journal = {Nature Genetics}, number = {1}, pages = {9 -- 10}, publisher = {Nature Publishing Group}, title = {{In search of the limits of evolution}}, doi = {10.1038/ng0105-9}, volume = {37}, year = {2005}, } @article{880, abstract = {Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution.}, author = {Kondrashov, Fyodor}, journal = {Biofizika}, number = {3}, pages = {396 -- 403}, publisher = {Pleiades Publishing}, title = {{The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus}}, volume = {50}, year = {2005}, } @article{882, abstract = {Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively.}, author = {Fyodor Kondrashov}, journal = {Human Molecular Genetics}, number = {16}, pages = {2415 -- 2419}, publisher = {Oxford University Press}, title = {{Prediction of pathogenic mutations in mitochondrially encoded human tRNAs}}, doi = {10.1093/hmg/ddi243}, volume = {14}, year = {2005}, } @article{893, abstract = {Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.}, author = {Jordan, Ingo K and Fyodor Kondrashov and Adzhubeǐ, Ivan A and Wolf, Yuri I and Koonin, Eugene V and Kondrashov, Alexey S and Sunyaev, Shamil R}, journal = {Nature}, number = {7026}, pages = {633 -- 638}, publisher = {Nature Publishing Group}, title = {{A universal trend of amino acid gain and loss in protein evolution}}, doi = {10.1038/nature03306}, volume = {433}, year = {2005}, } @article{8028, abstract = {Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.}, author = {Vogels, Tim P and Abbott, L. F.}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {46}, pages = {10786--10795}, publisher = {Society for Neuroscience}, title = {{Signal propagation and logic gating in networks of integrate-and-fire neurons}}, doi = {10.1523/jneurosci.3508-05.2005}, volume = {25}, year = {2005}, } @article{8029, abstract = {Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function.}, author = {Vogels, Tim P and Rajan, Kanaka and Abbott, L.F.}, issn = {0147-006X}, journal = {Annual Review of Neuroscience}, number = {1}, pages = {357--376}, publisher = {Annual Reviews}, title = {{Neural network dynamics}}, doi = {10.1146/annurev.neuro.28.061604.135637}, volume = {28}, year = {2005}, } @article{1740, abstract = {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.}, author = {Costantini, Giovanni and Rastelli, Armando and Manzano, Carlos and Acosta-Diaz, P and Georgios Katsaros and Songmuang, Rudeeson and Schmidt, Oliver G and Von Känel, Hans and Kern, Klaus}, journal = {Journal of Crystal Growth}, number = {1-4}, pages = {38 -- 45}, publisher = {Elsevier}, title = {{Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems}}, doi = {10.1016/j.jcrysgro.2004.12.047}, volume = {278}, year = {2005}, } @article{1741, abstract = {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.}, author = {Denker, Ulrich and Rastelli, Armando and Stoffel, Mathieu and Tersoff, Jerry and Georgios Katsaros and Costantini, Giovanni and Kern, Klaus and Jin-Phillipp, Neng Y and Jesson, David E and Schmidt, Oliver G}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Lateral motion of SiGe islands driven by surface-mediated alloying}}, doi = {10.1103/PhysRevLett.94.216103}, volume = {94}, year = {2005}, } @article{1742, abstract = {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.}, author = {Georgios Katsaros and Costantini, Giovanni and Stoffel, Mathieu and Esteban, Rubén and Bittner, Alexander M and Rastelli, Armando and Denker, Ulrich and Schmidt, Oliver G and Kern, Klaus}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {19}, publisher = {American Physical Society}, title = {{Kinetic origin of island intermixing during the growth of Ge on Si (001)}}, doi = {10.1103/PhysRevB.72.195320}, volume = {72}, year = {2005}, } @article{1743, abstract = {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.}, author = {Zhong, Zheyang and Georgios Katsaros and Stoffel, Mathieu and Costantini, Giovanni and Kern, Klaus and Schmidt, Oliver G and Jin-Phillipp, Neng Y and Bauer, Günther}, journal = {Applied Physics Letters}, number = {26}, pages = {1 -- 3}, publisher = {American Institute of Physics}, title = {{Periodic pillar structures by Si etching of multilayer GeSi/Si islands}}, doi = {10.1063/1.2150278}, volume = {87}, year = {2005}, } @article{1744, abstract = {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.}, author = {Georgios Katsaros and Darwazeh, Izzat Z and Lane, Phil M}, journal = {IEE Proceedings - Optoelectronics}, number = {6}, pages = {344 -- 352}, publisher = {Institute of Electrical Engineers}, title = {{Non linear transmission effects in duobinary and dicode optical systems}}, doi = {10.1049/ip-opt:20045067}, volume = {152}, year = {2005}, } @article{1795, abstract = {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.}, author = {Sandra Siegert and Thaler, Sonja and Wagner, Ralf and Schnierle, Barbara S}, journal = {AIDS Research and Therapy}, number = {1}, publisher = {BioMed Central}, title = {{Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors}}, doi = {10.1186/1742-6405-2-7}, volume = {2}, year = {2005}, } @article{1962, abstract = { 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.}, author = {Hinchliffe, Philip and Leonid Sazanov}, journal = {Science}, number = {5735}, pages = {771 -- 774}, publisher = {American Association for the Advancement of Science}, title = {{Biochemistry: Organization of iron-sulfur clusters in respiratory complex I}}, doi = {10.1126/science.1113988}, volume = {309}, year = {2005}, } @article{13431, abstract = {Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface topology of metals, glasses, and crystals. It is demonstrated that stamps soaked in an appropriate etchant can remove material with micrometer-scale precision. The Figure shows an array of concentric circles etched in glass using the immersion wet stamping process described (scale bar: 500 μm).}, author = {Smoukov, S. K. and Bishop, K. J. M. and Klajn, Rafal and Campbell, C. J. and Grzybowski, B. A.}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {11}, pages = {1361--1365}, publisher = {Wiley}, title = {{Cutting into solids with micropatterned gels}}, doi = {10.1002/adma.200402086}, volume = {17}, year = {2005}, } @article{13432, abstract = {A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers.}, author = {Campbell, Christopher J. and Klajn, Rafal and Fialkowski, Marcin and Grzybowski, Bartosz A.}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {1}, pages = {418--423}, publisher = {American Chemical Society}, title = {{One-step multilevel microfabrication by reaction−diffusion}}, doi = {10.1021/la0487747}, volume = {21}, year = {2005}, } @article{13433, abstract = {Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols.}, author = {Witt, Dariusz and Klajn, Rafal and Barski, Piotr and Grzybowski, Bartosz}, issn = {1875-5348}, journal = {Current Organic Chemistry}, keywords = {Organic Chemistry}, number = {18}, pages = {1763--1797}, publisher = {Bentham Science}, title = {{Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers}}, doi = {10.2174/1385272043369421}, volume = {8}, year = {2005}, } @inbook{1444, abstract = {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.}, author = {Tamas Hausel}, booktitle = {Geometric Methods in Algebra and Number Theory}, pages = {193 -- 217}, publisher = {Springer}, title = {{Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve}}, doi = {10.1007/0-8176-4417-2_9}, volume = {235}, year = {2005}, } @article{1447, abstract = {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.}, author = {Tamas Hausel}, journal = {Open Mathematics}, number = {1}, pages = {26 -- 38}, publisher = {Central European Science Journals}, title = {{Quaternionic geometry of matroids}}, doi = {10.2478/BF02475653}, volume = {3}, year = {2005}, } @article{1463, abstract = {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.}, author = {Tamas Hausel and Proudfoot, Nicholas J}, journal = {Topology}, number = {1}, pages = {231 -- 248}, publisher = {Elsevier}, title = {{Abelianization for hyperkähler quotients}}, doi = {10.1016/j.top.2004.04.002}, volume = {44}, year = {2005}, }