@article{2985, abstract = {The elimination voltammetry with linear scan (EVLS) was used to study adenine and cytosine reduction signals at the mercury electrode. In comparison with the linear scan voltammetry (which provides only one unresolved peak), two elimination functions provide good resolution of individual peaks and significant increase of sensitivity. The first elimination function eliminates the kinetic current (Ik) and conserves the diffusion current (Id). The second elimination function eliminates kinetic and charging currents (Ik and Ic) simultaneously and conserves the diffusion current (Id). Both functions give two well-resolved peaks of adenine and cytosine in a wide concentration range, while the linear sweep voltammetry gives badly resolved peaks due to hydrogen evolution. The best resolution of peaks is observed in acetate buffer at pH 3.8 and the detection limit for both substances is 500 nM. The concentration dependence of EVLS peak heights for one substance at the constant concentration of the other substance is linear. The peak potentials differ in these elimination functions. The difference in EVLS peak potentials gives the possibility to evaluate αna. Elimination voltammetry with linear scan contributes to the resolution of cathodic signals of purine and pyrimidine bases at very negative potentials near supporting electrolyte discharge. Copyright © 2001 Elsevier Science B.V.}, author = {Trnková, Libuše and Friml, Jirí and Dračka, Oldřich}, isbn = {1567-5394}, journal = {Bioelectrochemistry}, number = {2}, pages = {131 -- 136}, publisher = {Elsevier}, title = {{Elimination voltammetry of adenine and cytosine mixtures}}, doi = {10.1016/S1567-5394(01)00119-0}, volume = {54}, year = {2001}, } @inproceedings{3169, abstract = {Several new algorithms for visual correspondence based on graph cuts [7, 14, 17] have recently been developed. While these methods give very strong results in practice, they do not handle occlusions properly. Specifically, they treat the two input images asymmetrically, and they do not ensure that a pixel corresponds to at most one pixel in the other image. In this paper, we present a new method which properly addresses occlusions, while preserving the advantages of graph cut algorithms. We give experimental results for stereo as well as motion, which demonstrate that our method performs well both at detecting occlusions and computing disparities.}, author = {Kolmogorov, Vladimir and Zabih, Ramin}, booktitle = {Proceedings of the 8th IEEE International Conference on Computer Vision}, isbn = {0769511430}, location = {Vancouver, Canada}, pages = {508 -- 515}, publisher = {IEEE}, title = {{Computing visual correspondence with occlusions using graph cuts}}, doi = {10.1109/ICCV.2001.937668}, volume = {2}, year = {2001}, } @article{11125, abstract = {Although nuclear envelope (NE) assembly is known to require the GTPase Ran, the membrane fusion machinery involved is uncharacterized. NE assembly involves formation of a reticular network on chromatin, fusion of this network into a closed NE and subsequent expansion. Here we show that p97, an AAA-ATPase previously implicated in fusion of Golgi and transitional endoplasmic reticulum (ER) membranes together with the adaptor p47, has two discrete functions in NE assembly. Formation of a closed NE requires the p97–Ufd1–Npl4 complex, not previously implicated in membrane fusion. Subsequent NE growth involves a p97–p47 complex. This study provides the first insights into the molecular mechanisms and specificity of fusion events involved in NE formation.}, author = {HETZER, Martin W and Meyer, Hemmo H. and Walther, Tobias C. and Bilbao-Cortes, Daniel and Warren, Graham and Mattaj, Iain W.}, issn = {1476-4679}, journal = {Nature Cell Biology}, keywords = {Cell Biology}, number = {12}, pages = {1086--1091}, publisher = {Springer Nature}, title = {{Distinct AAA-ATPase p97 complexes function in discrete steps of nuclear assembly}}, doi = {10.1038/ncb1201-1086}, volume = {3}, year = {2001}, } @article{11755, abstract = {Hyperlink analysis algorithms significantly improve the relevance of the search results on the Web, so much so that all major Web search engines claim to use some type of hyperlink analysis. However, the search engines do not disclose details about the type of hyperlink analysis they perform, mostly to avoid manipulation of search results by Web-positioning companies. The article discusses how hyperlink analysis can be applied to ranking algorithms, and surveys other ways Web search engines can use this analysis.}, author = {Henzinger, Monika H}, issn = {1941-0131}, journal = {IEEE Internet Computing}, number = {1}, pages = {45--50}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Hyperlink analysis for the Web}}, doi = {10.1109/4236.895141}, volume = {5}, year = {2001}, } @article{841, author = {Wolf, Yuri and Kondrashov, Fyodor and Koonin, Eugene}, issn = {0168-9479}, journal = {Trends in Genetics}, number = {9}, pages = {499 -- 501}, publisher = {Elsevier}, title = {{Footprints of primordial introns on the eukaryotic genome: still no clear traces }}, doi = {10.1016/S0168-9525(01)02376-9}, volume = {17}, year = {2001}, } @article{851, abstract = {The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.}, author = {Rogozin, Igor and Kondrashov, Fyodor and Glazko, Galina}, issn = {1059-7794}, journal = {Human Mutation}, number = {2}, pages = {83 -- 102}, publisher = {Wiley-Blackwell}, title = {{Use of mutation spectra analysis software}}, doi = {10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E}, volume = {17}, year = {2001}, } @article{8521, abstract = {We continue the previous article's discussion of bounds, for prevalent diffeomorphisms of smooth compact manifolds, on the growth of the number of periodic points and the decay of their hyperbolicity as a function of their period $n$. In that article we reduced the main results to a problem, for certain families of diffeomorphisms, of bounding the measure of parameter values for which the diffeomorphism has (for a given period $n$) an almost periodic point that is almost nonhyperbolic. We also formulated our results for $1$-dimensional endomorphisms on a compact interval. In this article we describe some of the main techniques involved and outline the rest of the proof. To simplify notation, we concentrate primarily on the $1$-dimensional case.}, author = {Kaloshin, Vadim and Hunt, Brian R.}, issn = {1079-6762}, journal = {Electronic Research Announcements of the American Mathematical Society}, keywords = {General Mathematics}, number = {5}, pages = {28--36}, publisher = {American Mathematical Society}, title = {{A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II}}, doi = {10.1090/s1079-6762-01-00091-9}, volume = {7}, year = {2001}, } @article{8522, abstract = {For diffeomorphisms of smooth compact manifolds, we consider the problem of how fast the number of periodic points with period $n$grows as a function of $n$. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for $C^2$ or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call ``prevalence'', the growth is not much faster than exponential. Specifically, we show that for each $\delta > 0$, there is a prevalent set of ( $C^{1+\rho}$ or smoother) diffeomorphisms for which the number of period $n$ points is bounded above by $\operatorname{exp}(C n^{1+\delta})$ for some $C$ independent of $n$. We also obtain a related bound on the decay of the hyperbolicity of the periodic points as a function of $n$. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity shows this to be a subtle and complex phenomenon, reminiscent of KAM theory.}, author = {Kaloshin, Vadim and Hunt, Brian R.}, issn = {1079-6762}, journal = {Electronic Research Announcements of the American Mathematical Society}, keywords = {General Mathematics}, number = {4}, pages = {17--27}, publisher = {American Mathematical Society}, title = {{A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I}}, doi = {10.1090/s1079-6762-01-00090-7}, volume = {7}, year = {2001}, } @article{8524, abstract = {A number α∈R is diophantine if it is not well approximable by rationals, i.e. for some C,ε>0 and any relatively prime p,q∈Z we have |αq−p|>Cq−1−ε. It is well-known and is easy to prove that almost every α in R is diophantine. In this paper we address a noncommutative version of the diophantine properties. Consider a pair A,B∈SO(3) and for each n∈Z+ take all possible words in A, A -1, B, and B - 1 of length n, i.e. for a multiindex I=(i1,i1,…,im,jm) define |I|=∑mk=1(|ik|+|jk|)=n and \( W_n(A,B ) = \{W_{\cal I}(A,B) = A^{i_1} B^{j_1} \dots A^{i_m} B^{j_m}\}_{|{\cal I|}=n \).¶Gamburd—Jakobson—Sarnak [GJS] raised the problem: prove that for Haar almost every pair A,B∈SO(3) the closest distance of words of length n to the identity, i.e. sA,B(n)=min|I|=n∥WI(A,B)−E∥, is bounded from below by an exponential function in n. This is the analog of the diophantine property for elements of SO(3). In this paper we prove that s A,B (n) is bounded from below by an exponential function in n 2. We also exhibit obstructions to a “simple” proof of the exponential estimate in n.}, author = {Kaloshin, Vadim and Rodnianski, I.}, issn = {1016-443X}, journal = {Geometric And Functional Analysis}, number = {5}, pages = {953--970}, publisher = {Springer Nature}, title = {{Diophantine properties of elements of SO(3)}}, doi = {10.1007/s00039-001-8222-8}, volume = {11}, year = {2001}, } @article{855, abstract = {Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing.}, author = {Rogozin, Igor and Kochetov, Alex and Kondrashov, Fyodor and Koonin, Eugene and Milanesi, Luciano}, issn = {1367-4803}, journal = {Bioinformatics}, number = {10}, pages = {890 -- 900}, publisher = {Oxford University Press}, title = {{Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon}}, doi = {10.1093/bioinformatics/17.10.890}, volume = {17}, year = {2001}, } @article{867, abstract = {Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes.}, author = {Kondrashov, Fyodor and Koonin, Eugene}, issn = {0964-6906}, journal = {Human Molecular Genetics}, number = {23}, pages = {2661 -- 2669}, publisher = {Oxford University Press}, title = {{Origin of alternative splicing by tandem exon duplication}}, doi = {10.1093/hmg/10.23.2661}, volume = {10}, year = {2001}, } @article{874, abstract = {Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability.}, author = {Kondrashov, Fyodor and Kondrashov, Alexey}, issn = {0027-8424}, journal = {PNAS}, number = {21}, pages = {12089 -- 12092}, publisher = {National Academy of Sciences}, title = {{Multidimensional epistasis and the disadvantage of sex}}, doi = {10.1073/pnas.211214298}, volume = {98}, year = {2001}, } @article{888, abstract = {BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.}, author = {Jordan, Ingo and Kondrashov, Fyodor and Rogozin, Igor and Tatusov, Roman and Wolf, Yuri and Koonin, Eugene}, issn = {1465-6906}, journal = {Genome Biology}, number = {12}, publisher = {BioMed Central}, title = {{Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins }}, doi = {10.1186/gb-2001-2-12-research0053}, volume = {2}, year = {2001}, } @inproceedings{2340, abstract = {Recent experimental breakthroughs in the treatment of dilute Bose gases have renewed interest in their quantum mechanical description, respectively in approximations to it. The ground state properties of dilute Bose gases confined in external potentials and interacting via repulsive short range forces are usually described by means of the Gross-Pitaevskii energy functional. In joint work with Elliott H. Lieb and Jakob Yngvason its status as an approximation for the quantum mechanical many-body ground state problem has recently been rigorously clarified. We present a summary of this work, for both the two-and three-dimensional case. }, author = {Seiringer, Robert}, editor = {Demuth, Michael and Schultze, Bert}, isbn = {9783034894838}, location = {Clausthal, Germany}, pages = {307 -- 314}, publisher = {Birkhäuser}, title = {{Bosons in a trap: Asymptotic exactness of the Gross-Pitaevskii ground state energy formula}}, doi = {10.1007/978-3-0348-8231-6}, volume = {126}, year = {2001}, } @article{2341, abstract = {We study the ground state properties of an atom with nuclear charge Z and N bosonic "electrons" in the presence of a homogeneous magnetic field B. We investigate the mean field limit N→∞ with N / Z fixed, and identify three different asymptotic regions, according to B≪Z2,B∼Z2,andB≫Z2 . In Region 1 standard Hartree theory is applicable. Region 3 is described by a one-dimensional functional, which is identical to the so-called Hyper-Strong functional introduced by Lieb, Solovej and Yngvason for atoms with fermionic electrons in the region B≫Z3 ; i.e., for very strong magnetic fields the ground state properties of atoms are independent of statistics. For Region 2 we introduce a general magnetic Hartree functional, which is studied in detail. It is shown that in the special case of an atom it can be restricted to the subspace of zero angular momentum parallel to the magnetic field, which simplifies the theory considerably. The functional reproduces the energy and the one-particle reduced density matrix for the full N-particle ground state to leading order in N, and it implies the description of the other regions as limiting cases.}, author = {Baumgartner, Bernhard and Seiringer, Robert}, issn = {1424-0637}, journal = {Annales Henri Poincare}, number = {1}, pages = {41 -- 76}, publisher = {Birkhäuser}, title = {{Atoms with bosonic "electrons" in strong magnetic fields}}, doi = {10.1007/PL00001032}, volume = {2}, year = {2001}, } @article{2345, abstract = {We give upper bounds for the number of spin-1/2 particles that can be bound to a nucleus of charge Z in the presence of a magnetic field B, including the spin-field coupling. We use Lieb's strategy, which is known to yield Nc < 2Z + 1 for magnetic fields that go to zero at infinity, ignoring the spin-field interaction. For particles with fermionic statistics in a homogeneous magnetic field our upper bound has an additional term of the order of Z × min {(B/Z3)2/5, 1 + | 1n(B/Z3)|2}.}, author = {Seiringer, Robert}, issn = {0305-4470}, journal = {Journal of Physics A: Mathematical and General}, number = {9}, pages = {1943 -- 1948}, publisher = {IOP Publishing Ltd.}, title = {{On the maximal ionization of atoms in strong magnetic fields}}, doi = {10.1088/0305-4470/34/9/311}, volume = {34}, year = {2001}, } @article{2346, abstract = {By means of a generalization of the Fefferman - de la Llave decomposition we derive a general lower bound on the interaction energy of one-dimensional quantum systems. We apply this result to a specific class of lowest Landau band wave functions.}, author = {Hainzl, Christian and Seiringer, Robert}, issn = {0377-9017}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {133 -- 142}, publisher = {Springer}, title = {{Bounds on one-dimensional exchange energies with application to lowest Landau band quantum mechanics}}, doi = {10.1023/A:1010951905548}, volume = {55}, year = {2001}, } @article{2347, abstract = {We consider the ground state properties of an inhomogeneous two-dimensional Bose gas with a repulsive, short range pair interaction and an external confining potential. In the limit when the particle number N is large but ρ̅a 2 is small, where ρ̅ is the average particle density and a the scattering length, the ground state energy and density are rigorously shown to be given to leading order by a Gross–Pitaevskii (GP) energy functional with a coupling constant g~1/|1n(ρ̅a 2)|. In contrast to the 3D case the coupling constant depends on N through the mean density. The GP energy per particle depends only on Ng. In 2D this parameter is typically so large that the gradient term in the GP energy functional is negligible and the simpler description by a Thomas–Fermi type functional is adequate.}, author = {Lieb, Élliott and Seiringer, Robert and Yngvason, Jakob}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {17 -- 31}, publisher = {Springer}, title = {{A rigorous derivation of the Gross-Pitaevskii energy functional for a two-dimensional Bose gas}}, doi = {10.1007/s002200100533}, volume = {224}, year = {2001}, } @article{2348, abstract = {This paper concerns the asymptotic ground state properties of heavy atoms in strong, homogeneous magnetic fields. In the limit when the nuclear charge Z tends to ∞ with the magnetic field B satisfying B ≫ Z4/3 all the electrons are confined to the lowest Landau band. We consider here an energy functional, whose variable is a sequence of one-dimensional density matrices corresponding to different angular momentum functions in the lowest Landau band. We study this functional in detail and derive various interesting properties, which are compared with the density matrix (DM) theory introduced by Lieb, Solovej and Yngvason. In contrast to the DM theory the variable perpendicular to the field is replaced by the discrete angular momentum quantum numbers. Hence we call the new functional a discrete density matrix (DDM) functional. We relate this DDM theory to the lowest Landau band quantum mechanics and show that it reproduces correctly the ground state energy apart from errors due to the indirect part of the Coulomb interaction energy.}, author = {Hainzl, Christian and Seiringer, Robert}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {229 -- 248}, publisher = {Springer}, title = {{A discrete density matrix theory for atoms in strong magnetic fields}}, doi = {10.1007/s002200100373}, volume = {217}, year = {2001}, } @article{2419, abstract = {For an absolutely continuous probability measure μ. on ℝd and a nonnegative integer k, let S̃k(μ, 0) denote the probability that the convex hull of k + d + 1 random points which are i.i.d. according to μ contains the origin 0. For d and k given, we determine a tight upper bound on S̃k(μ, 0), and we characterize the measures in ℝd which attain this bound. As we will see, this result can be considered a continuous analogue of the Upper Bound Theorem for the maximal number of faces of convex polytopes with a given number of vertices. For our proof we introduce so-called h-functions, continuous counterparts of h-vectors of simplicial convex polytopes.}, author = {Wagner, Uli and Welzl, Emo}, issn = {0179-5376}, journal = {Discrete & Computational Geometry}, number = {2}, pages = {205 -- 219}, publisher = {Springer}, title = {{A continuous analogue of the Upper Bound Theorem}}, doi = {10.1007/s00454-001-0028-9}, volume = {26}, year = {2001}, }