@article{3622, abstract = {The extent of genetic variation in fitness and its components and genetic variation's dependence on environmental conditions remain key issues in evolutionary biology. We present measurements of genetic variation in preadult viability in a laboratory-adapted population of Drosophila melanogaster, made at four different densities. By crossing flies heterozygous for a wild-type chromosome and one of two different balancers (TM1, TM2), we measure both heterozygous (TM1/+, TM2/+) and homozygous (+/+) viability relative to a standard genotype (TM1/TM2). Forty wild-type chromosomes were tested, of which 10 were chosen to be homozygous viable. The mean numbers produced varied significantly between chromosome lines, with an estimated between-line variance in loge numbers of 0.013. Relative viabilities also varied significantly across chromosome lines, with a variance in loge homozygous viability of 1.76 and of loge heterozygous viability of 0.165. The between-line variance for numbers emerging increased with density, from 0.009 at lowest density to 0.079 at highest. The genetic variance in relative viability increases with density, but not significantly. Overall, the effects of different chromosomes on relative viability were remarkably consistent across densities and across the two heterozygous genotypes (TM1, TM2). The 10 lines that carried homozygous viable wild-type chromosomes produced significantly more adults than the 30 lethal lines at low density and significantly fewer adults at the highest density. Similarly, there was a positive correlation between heterozygous viability and mean numbers at low density, but a negative correlation at high density.}, author = {Gardner, Michael and Fowler, Kevin and Patridge, Linda and Barton, Nicholas H}, issn = {0014-3820}, journal = {Evolution}, number = {8}, pages = {1609 -- 1620}, publisher = {Wiley-Blackwell}, title = {{Genetic variation for preadult viability in Drosophila melanogaster}}, doi = {10.1111/j.0014-3820.2001.tb00680.x}, volume = {55}, year = {2001}, } @misc{3596, author = {Barton, Nicholas H}, booktitle = {Trends in Genetics}, issn = {0168-9479}, pages = {420 -- 420}, publisher = {Elsevier}, title = {{Mendel and mathematics}}, doi = {10.1016/S0168-9525(01)02315-0}, volume = {17}, year = {2001}, } @article{3546, abstract = {Local versus distant coherence of hippocampal CA1 pyramidal cells was investigated in the behaving rat. Temporal cross-correlation of pyramidal cells revealed a significantly stronger relationship among local (<140 <mu>m) pyramidal neurons compared with distant (>300 mum) neurons during non-theta-associated immobility and sleep but not during theta-associated running and walking. In contrast, cross-correlation between local pyramidal cell-interneuron pairs was significantly stronger than between distant pairs during theta oscillations but were similar during non-theta-associated behaviors. We suggest that network state-dependent functional clustering of neuronal activity emerges because of the differential contribution of the main excitatory inputs, the perforant path, and Schaffer collaterals during theta and non-theta behaviors.}, author = {Hirase, Hajima and Leinekugel, Xavier and Csicsvari, Jozsef L and Czurkó, András and Buzsáki, György}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {10}, publisher = {Society for Neuroscience}, title = {{Behavior-dependent states of the hippocampal network affect functional clustering of neurons}}, doi = {10.1523/JNEUROSCI.21-10-j0003.2001}, volume = {21}, year = {2001}, } @article{3540, abstract = {What determines the firing rate of cortical neurons in the absence of external sensory input or motor behavior, such as during sleep? Hero we report that, in a familiar environment, the discharge frequency of simultaneously recorded individual CA1 pyramidal neurons and the coactivation of cell pairs remain highly correlated across sleep-wake-steep sequences. However, both measures were affected when new sets of neurons were activated in a novel environment. Nevertheless, the grand mean firing rate of the whole pyramidal cell population remained constant across behavioral states and testing conditions. The findings suggest that long-term firing patterns of single cells can be modified by experience. We hypothesize that increased firing rates of recently used neurons are associated with a concomitant decrease in the discharge activity of the remaining population, leaving the mean excitability of the hippocampal network unaltered.}, author = {Hirase, Hajima and Leinekugel, Xavier and Czurkó, András and Csicsvari, Jozsef L and Buzsáki, György}, issn = {0027-8424}, journal = {PNAS}, number = {16}, pages = {9386 -- 9390}, publisher = {National Academy of Sciences}, title = {{Firing rates of hippocampal neurons are preserved during subsequent sleep episodes and modified by novel awake experience}}, doi = {10.1073/pnas.161274398}, volume = {98}, year = {2001}, } @article{3494, abstract = {Mutual synaptic interactions between GABAergic interneurons are thought to be of critical importance for the generation of network oscillations and for temporal encoding of information in the hippocampus. However, the functional properties of synaptic transmission between hippocampal interneurons are largely unknown. We have made paired recordings from basket cells (BCs) in the dentate gyrus of rat hippocampal slices, followed by correlated light and electron microscopical analysis. Unitary GABAAreceptor-mediated IPSCs at BC–BC synapses recorded at the soma showed a fast rise and decay, with a mean decay time constant of 2.5 ± 0.2 msec (32°C). Synaptic transmission at BC–BC synapses showed paired-pulse depression (PPD) (32 ± 5% for 10 msec interpulse intervals) and multiple-pulse depression during repetitive stimulation. Detailed passive cable model simulations based on somatodendritic morphology and localization of synaptic contacts further indicated that the conductance change at the postsynaptic site was even faster, decaying with a mean time constant of 1.8 ± 0.6 msec. Sequential triple recordings revealed that the decay time course of IPSCs at BC–BC synapses was approximately twofold faster than that at BC–granule cell synapses, whereas the extent of PPD was comparable. To examine the consequences of the fast postsynaptic conductance change for the generation of oscillatory activity, we developed a computational model of an interneuron network. The model showed robust oscillations at frequencies >60 Hz if the excitatory drive was sufficiently large. Thus the fast conductance change at interneuron–interneuron synapses may promote the generation of high-frequency oscillations observed in the dentate gyrusin vivo. }, author = {Bartos, Marlene and Vida, Imre and Frotscher, Michael and Geiger, Jörg and Jonas, Peter M}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {8}, pages = {2687 -- 2698}, publisher = {Society for Neuroscience}, title = {{Rapid signaling at inhibitory synapses in a dentate gyrus interneuron network.}}, doi = {10.1523/JNEUROSCI.21-08-02687.2001}, volume = {21}, year = {2001}, } @article{3496, abstract = {The mossy fiber-CA3 pyramidal neuron synapse is a main component of the hippocampal trisynaptic circuitry. Recent studies, however, suggested that inhibitory interneurons are the major targets of the mossy fiber system. To study the regulation of mossy fiber-interneuron excitation, we examined unitary and compound excitatory postsynaptic currents in dentate gyrus basket cells, evoked by paired recording between granule and basket cells or extracellular stimulation of mossy fiber collaterals. The application of an associative high-frequency stimulation paradigm induced posttetanic potentiation (PTP) followed by homosynaptic long-term potentiation (LTP). Analysis of numbers of failures, coefficient of variation, and paired-pulse modulation indicated that both PTP and LTP were expressed presynaptically. The Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA) did not affect PTP or LTP at a concentration of 10 mM but attenuated LTP at a concentration of 30 mM. Both forskolin, an adenylyl cyclase activator, and phorbolester diacetate, a protein kinase C stimulator, lead to a long-lasting increase in excitatory postsynaptic current amplitude. H-89, a protein kinase A inhibitor, and bisindolylmaleimide, a protein kinase C antagonist, reduced PTP, whereas only bisindolylmaleimide reduced LTP. These results may suggest a differential contribution of protein kinase A and C pathways to mossy fiber-interneuron plasticity. Interneuron PTP and LTP may provide mechanisms to maintain the balance between synaptic excitation of interneurons and that of principal neurons in the dentate gyrus-CA3 network. }, author = {Alle, Henrik and Jonas, Peter M and Geiger, Jörg}, issn = {0027-8424}, journal = {PNAS}, number = {25}, pages = {14708 -- 14713}, publisher = {National Academy of Sciences}, title = {{PTP and LTP at a hippocampal mossy fiber-interneuron synapse}}, doi = {10.1073/pnas.251610898 }, volume = {98}, year = {2001}, } @article{3495, abstract = {High Ca2+ permeability and its control by voltage-dependent Mg2+ block are defining features of NMDA receptors. These features are lost if the principal NR1 subunit carries an asparagine (N) to arginine (R) substitution in a critical channel site at NR1 position 598. NR1(R) expression from a single allele in gene-targeted NR1+/R mice is lethal soon after birth, precluding analysis of altered synaptic functions later in life. We therefore employed the forebrain specific αCaMKII promoter to drive tTA-mediated tetracyclin sensitive transcription of transgenes for NR1(R) and for lacZ as reporter. Transgene expression was observed in cortex, striatum, hippocampus, amygdala and olfactory bulb and was mosaic in all these forebrain regions. It was highest in olfactory bulb granule cells, in most of which Ca2+ permeability and voltage-dependent Mg2+ block of NMDA receptors were reduced to different extents. This indicates significant impairment of NMDA receptor function by NR1(R) in presence of the wild-type NR1 complement. Indeed, even though NR1(R) mRNA constituted only 18% of the entire NR1 mRNA population in forebrain, the transgenic mice died during adolescence unless transgene expression was suppressed by doxycycline. Thus, glutamate receptor function can be altered in the mouse by regulated NR1(R) transgene expression.}, author = {Jerecic, Jasna and Schulze, Christian and Jonas, Peter M and Sprengel, Rolf and Seeburg, Peter and Bischofberger, Joseph}, issn = {0169-328X}, journal = {Molecular Brain Research}, number = {1-2}, pages = {96 -- 104}, publisher = {Elsevier}, title = {{Impaired NMDA receptor function in mouse olfactory bulb neurons by tetracycline-sensitive NR1 (N598R) expression}}, doi = {10.1016/S0169-328X(01)00221-2}, volume = {94}, year = {2001}, } @article{3517, abstract = {A modular multichannel microdrive ('hyperdrive') is described. The microdrive uses printed circuit board technology and flexible fused silica capillaries. The modular design allows for the fabrication of 4-32 independently movable electrodes or `tetrodes'. The drives are re-usable and re-loading the drive with electrodes is simple. }, author = {Szabo, Imre and Czurkó, András and Csicsvari, Jozsef L and Hirase, Hajima and Leinekugel, Xavier and Buzsáki, György}, issn = {0165-0270}, journal = {Journal of Neuroscience Methods}, number = {1}, pages = {105 -- 110}, publisher = {Elsevier}, title = {{The application of printed circuit board technology for fabrication of multi-channel micro-drives}}, doi = {10.1016/S0165-0270(00)00362-9}, volume = {105}, year = {2001}, } @article{3493, abstract = {Although agonists and competitive antagonists presumably occupy overlapping binding sites on ligand-gated channels, these interactions cannot be identical because agonists cause channel opening whereas antagonists do not. One explanation is that only agonist binding performs enough work on the receptor to cause the conformational changes that lead to gating. This idea is supported by agonist binding rates at GABAA and nicotinic acetylcholine receptors that are slower than expected for a diffusion-limited process, suggesting that agonist binding involves an energy-requiring event. This hypothesis predicts that competitive antagonist binding should require less activation energy than agonist binding. To test this idea, we developed a novel deconvolution-based method to compare binding and unbinding kinetics of GABAA receptor agonists and antagonists in outside-out patches from rat hippocampal neurons. Agonist and antagonist unbinding rates were steeply correlated with affinity. Unlike the agonists, three of the four antagonists tested had binding rates that were fast, independent of affinity, and could be accounted for by diffusion- and dehydration-limited processes. In contrast, agonist binding involved additional energy-requiring steps, consistent with the idea that channel gating is initiated by agonist-triggered movements within the ligand binding site. Antagonist binding does not appear to produce such movements, and may in fact prevent them.}, author = {Jones, M.V and Jonas, Peter M and Sahara, Y. and Westbrook, G.}, issn = {0006-3495}, journal = {Biophysical Journal}, number = {5}, pages = {2660 -- 2670}, publisher = {Biophysical Society}, title = {{Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists}}, doi = {10.1016/S0006-3495(01)75909-7 }, volume = {81}, year = {2001}, } @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{3439, abstract = {High molecular weight DNA was extracted from the primary Neotropical malaria vector, Anopheles darlingi from Capanema, Pará, Brazil, to create a small insert genomic library, and then a phagemid library. Enriched sublibraries were constructed from the phagemid library using a microsatellite oligo primed second strand synthesis protocol. The resulting 242 760 individual clones were screened. The mean clone size of the positive clones was 302 bp. Flanking primers were designed for each suitable microsatellite sequence. Eight polymorphic loci were optimized and characterized. The allele size ranges are based on 253 samples of A. darlingi from eastern Amazonian and central Brazil.}, author = {Conn, Jan and Bollback, Jonathan P and Onyabe, David and Robinson, Tessa and Wilkerson, Richard and Povoa, Marinete}, issn = {1471-8278}, journal = {Molecular Ecology Notes}, number = {4}, pages = {223 -- 225}, publisher = {Wiley-Blackwell}, title = {{Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi}}, doi = { 10.1046/j.1471-8278.2001.00078.x}, volume = {1}, year = {2001}, } @article{3440, abstract = {Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis. }, author = {Huelsenbeck, John and Bollback, Jonathan P}, issn = {0039-7989}, journal = {Systematic Biology}, number = {3}, pages = {351 -- 366}, publisher = {Oxford University Press}, title = {{Empirical and hierarchical Bayesian estimation of ancestral states}}, doi = {10.1080/10635150119871}, volume = {50}, year = {2001}, } @article{3438, abstract = {As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.}, author = {Huelsenbeck, John and Ronquist, Fredrik and Nielsen, Rasmus and Bollback, Jonathan P}, issn = {0036-8075}, journal = {Science}, number = {5550}, pages = {2310 -- 2314}, publisher = {American Association for the Advancement of Science}, title = {{Bayesian inference of phylogeny and its impact on evolutionary biology}}, doi = {10.1126/science.1065889}, volume = {294}, year = {2001}, } @inbook{3434, abstract = {This chapter contains sections titled: Introduction - History - Developing an Intuition of Likelihood - Method of Maximum Likelihood - Bayesian Inference - Markov Chain Monte Carlo - Assessing Uncertainty of Phylogenies - Hypothesis Testing and Model Choice - Comparative Analysis - Conclusions - References}, author = {Huelsenbeck, John and Bollback, Jonathan P}, booktitle = {Handbook of Statistical Genetics}, editor = {Balding, David and Bishop, Martin and Cannings, Chriss}, isbn = {9781119429142 }, pages = {415 -- 439}, publisher = {Wiley-Blackwell}, title = {{Application of the likelihood function in phylogenetic analysis}}, doi = {10.1002/9780470061619.ch15}, year = {2001}, } @article{2982, abstract = {Polar auxin transport is crucial for the regulation of auxin action and required for some light-regulated responses during plant development. We have found that two mutants of Arabidopsis - doc1, which displays altered expression of light-regulated genes, and tir3, known for its reduced auxin transport - have similar defects and define mutations in a single gene that we have renamed BIG. BIG is very similar to the Drosophila gene Calossin/Pushover, a member of a gene family also present in Caenorhabditis elegans and human genomes. The protein encoded by BIG is extraordinary in size, 560 kD, and contains several putative Zn-finger domains. Expression-profiling experiments indicate that altered expression of multiple light-regulated genes in doc1 mutants can be suppressed by elevated levels of auxin caused by overexpression of an auxin biosynthetic gene, suggesting that normal auxin distribution is required to maintain low-level expression of these genes in the dark. Double mutants of tir3 with the auxin mutants pin1, pid, and axr1 display severe defects in auxin-dependent growth of the inflorescence. Chemical inhibitors of auxin transport change the intracellular localization of the auxin efflux carrier PIN1 in doc1/tir3 mutants, supporting the idea that BIG is required for normal auxin efflux.}, author = {Gil, Pedro and Dewey, Elizabeth and Friml, Jirí and Zhao, Yunde and Snowden, Kimberley and Putterill, Jo and Palme, Klaus and Estelle, Mark and Chory, Joanne}, issn = {0890-9369}, journal = {Genes and Development}, number = {15}, pages = {1985 -- 1997}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{BIG: A calossin-like protein required for polar auxin transport in Arabidopsis}}, doi = {10.1101/gad.905201}, volume = {15}, year = {2001}, } @article{2984, abstract = {Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has been assumed to represent the sole mode of long distance IAA movement. Localization of the auxin permease AUX1 in the Arabidopsis root apex has revealed a novel phloem-based IAA transport pathway. AUX1, asymmetrically localized to the plasma membrane of root protophloem cells, is proposed to promote the acropetal, post-phloem movement of auxin to the root apex. MS analysis shows that IAA accumulation in aux1 mutant root apices is impaired, consistent with an AUX1 phloem unloading function. AUX1 localization to columella and lateral root cap tissues of the Arabidopsis root apex reveals that the auxin permease regulates a second IAA transport pathway. Expression studies using an auxin-regulated reporter suggest that AUX1 is necessary for root gravitropism by facilitating basipetal auxin transport to distal elongation zone tissues.}, author = {Swarup, Ranjan and Friml, Jirí and Marchant, Alan and Ljung, Karin and Sandberg, Göran and Palme, Klaus and Bennett, Malcolm}, issn = {Genes and Development}, journal = {Genes and Development}, number = {20}, pages = {2648 -- 2653}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex}}, doi = {10.1101/gad.210501}, volume = {15}, year = {2001}, } @article{2981, abstract = {Plants contain a novel unique subfamily of Rho GTPases, vital components of cellular signalling networks. Here we report a general role for some members of this family in polarized plant growth processes. We show that Arabidopsis AtRop4 and AtRop6 encode functional GTPases with similar intrinsic GTP hydrolysis rates. We localized AtRop proteins in root meristem cells to the cross-wall and cell plate membranes. Polar localization of AtRops in trichoblasts specifies the growth sites for emerging root hairs. These sites were visible before budding and elongation of the Arabidopsis root hair when AtRops accumulated at their tips. Expression of constitutively active AtRop4 and AtRop6 mutant proteins in root hairs of transgenic Arabidopsis plants abolished polarized growth and delocalized the tip-focused Ca2+ gradient. Polar localization of AtRops was inhibited by brefeldin A, but not by other drugs such as latrunculin B, cytochalasin D or caffeine. Our results demonstrate a general function of AtRop GTPases in tip growth and in polar diffuse growth.}, author = {Molendijk, Arthur and Bischoff, Friedrich and Rajendrakumar, Chadalavada and Friml, Jirí and Braun, Markus and Gilroy, Simon and Palme, Klaus}, issn = {0261-4189}, journal = {EMBO Journal}, number = {11}, pages = {2779 -- 2788}, publisher = {Wiley-Blackwell}, title = {{Arabidopsis thaliana Rop GTPases are localized to tips of root hairs and control polar growth}}, doi = {10.1093/emboj/20.11.2779}, volume = {20}, year = {2001}, } @article{2983, abstract = {Polar transport of the phytohormone auxin mediates various processes in plant growth and development, such as apical dominance, tropisms, vascular patterning and axis formation. This view is based largely on the effects of polar auxin transport inhibitors. These compounds disrupt auxin efflux from the cell but their mode of action is unknown. It is thought that polar auxin flux is caused by the asymmetric distribution of efflux carriers acting at the plasma membrane. The polar localization of efflux carrier candidate PIN1 supports this model. Here we show that the seemingly static localization of PIN1 results from rapid actin-dependent cycling between the plasma membrane and endosomal compartments. Auxin transport inhibitors block PIN1 cycling and inhibit trafficking of membrane proteins that are unrelated to auxin transport. Our data suggest that PIN1 cycling is of central importance for auxin transport and that auxin transport inhibitors affect efflux by generally interfering with membrane-trafficking processes. In support of our conclusion, the vesicle-trafficking inhibitor brefeldin A mimics physiological effects of auxin transport inhibitors.}, author = {Geldner, Niko and Friml, Jirí and Stierhof, York and Jürgens, Gerd and Palme, Klaus}, issn = {0028-0836}, journal = {Nature}, number = {6854}, pages = {425 -- 428}, publisher = {Nature Publishing Group}, title = {{Auxin transport inhibitors block PIN1 cycling and vesicle trafficking}}, doi = {10.1038/35096571}, volume = {413}, year = {2001}, } @article{2736, abstract = {We consider the time evolution of N bosonic particles interacting via a mean field Coulomb potential. Suppose the initial state is a product wavefunction. We show that at any finite time the correlation functions factorize in the limit N → ∞. Furthermore, the limiting one particle density matrix satisfies the nonlinear Hartree equation. The key ingredients are the uniqueness of the BBGKY hierarchy for the correlation functions and a new apriori estimate for the many-body Schrödinger equations.}, author = {Erdös, László and Yau, Horng}, issn = {1095-0761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {6}, pages = {1169 -- 1205}, publisher = {International Press}, title = {{Derivation of the nonlinear Schrödinger equation from a many body Coulomb system}}, doi = {10.48550/arXiv.math-ph/0111042}, volume = {5}, year = {2001}, } @article{2735, abstract = {We establish the exact low-energy asymptotics of the integrated density of states (Lifschitz tail) in a homogeneous magnetic field and Poissonian impurities with a repulsive single-site potential of Gaussian decay. It has been known that the Gaussian potential tail discriminates between the so-called “classical” and “quantum” regimes, and precise asymptotics are known in these cases. For the borderline case, the coexistence of the classical and quantum regimes was conjectured. Here we settle this last remaining open case to complete the full picture of the magnetic Lifschitz tails.}, author = {Erdös, László}, issn = {0044-3719}, journal = {Probability Theory and Related Fields}, number = {2}, pages = {219 -- 236}, publisher = {Springer}, title = {{Lifschitz tail in a magnetic field: Coexistence of classical and quantum behavior in the borderline case}}, doi = {10.1007/PL00008803}, volume = {121}, year = {2001}, } @article{2734, abstract = {In this paper we describe an intrinsically geometric way of producing magnetic fields on S3 and R3 for which the corresponding Dirac operators have a non-trivial kernel. In many cases we are able to compute the dimension of the kernel. In particular we can give examples where the kernel has any given dimension. This generalizes the examples of Loss and Yau [1].}, author = {Erdös, László and Solovej, Jan}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {10}, pages = {1247 -- 1280}, publisher = {World Scientific Publishing}, title = {{The kernel of Dirac operators on S3 and R3}}, doi = {10.1142/S0129055X01000983}, volume = {13}, year = {2001}, } @article{2611, abstract = {Research using animal models of neuropathic pain has revealed sympathetic sprouting onto dorsal root ganglion cells. More recently, sensory fibre sprouting onto dorsal root ganglion cells has also been observed. Previous work in our laboratory demonstrated persistent sympathetic fibre sprouting in the skin of the rat lower lip following sensory denervation of this region. Therefore, we applied immunocytochemistry to determine the effects of sympathectomies on the terminal fields of sensory fibres. The superior cervical ganglia were removed bilaterally and the effects on the innervation of the skin of the rat lower lip were observed 1, 2, 3, 4, 6 and 8 weeks post-surgery. Substance P and dopamine-β-hydroxylase immunoreactivities were used to identify a subset of sensory and sympathetic fibres, respectively. We also assessed neurokinin-1 receptor immunoreactivity. Quantitative data was obtained with the aid of an image analysis system. In controls, the epidermis and upper dermis were innervated by substance P-immunoreactive fibres only and upper dermal blood vessels possessed the highest density of neurokinin-1 receptor immunoreactivity. Blood vessels in the lower dermis were innervated by both substance P- and dopamine-β-hydroxylase-immunoreactive fibres. Following sympathectomies, substance P-immunoreactive fibres in the epidermis and upper dermis were more intensely labelled only 1 and 2 weeks post-surgery when compared to sham controls. The length of substance P-immunoreactive fibres in this region was also increased only on the second week. Neurokinin-1 receptor immunoreactivity in the upper dermis was slightly decreased 1 and 2 weeks post-surgery. In the lower dermis, substance P-immunoreactive fibres associated with blood vessels were more intensely labelled only 1 and 2 weeks post-surgery, and at all post-surgical time points studied, blood vessels in this region were devoid of dopamine-β-hydroxylase-immunoreactive fibres. The length of substance P-immunoreactive fibres was increased from the first to the third week post-surgery in the lower dermis. These results indicate that sympathectomies lead to transient changes in substance P-immunoreactive fibre innervation and neurokinin-1 receptor expression in rat lower lip skin. The effects are most prominent in the lower dermis probably due to a greater local concentration of nerve growth factor in this region. The plasticity of the interactions between sensory and sympathetic fibres may prove important in the regulation of skin microcirculation and in the generation of painful sensations under normal conditions or following peripheral nerve injuries.}, author = {Ruocco, Isabella and Cuello, Augusto and Shigemoto, Ryuichi and Ribeiro Da Silva, Alfredo}, issn = {0306-4522}, journal = {Neuroscience}, number = {1}, pages = {157 -- 166}, publisher = {Elsevier}, title = {{Sympathectomies lead to transient substance P-immunoreactive sensory fibre plasticity in the rat skin}}, doi = {10.1016/S0306-4522(01)00158-0}, volume = {108}, year = {2001}, } @article{2612, abstract = {We examined immunoreactivities for γ-aminobutyric acidB-receptor (GABABR) subtypes, GABABR1 and GABABR2, in the mesencephalic trigeminal nucleus neurons (MTN neurons) of the rat. Immunoreactivity for GABABR1 was prominent in cell bodies of MTN, whereas that for GABABR2 was very weak, if existed. For electron microscopy, the immunogold-silver method for GABABR1 was combined with the immunoperoxidase method for glutamic acid decarboxylase (GAD: the synthetic enzyme of GABA). Immunogold-silver particles indicating GABABR1 immunoreactivity were distributed widely in the cytoplasm of the cell bodies postsynaptic to GAD-immunoreactive axon terminals, but were rarely associated with synaptic membrane specialization or extrasynaptic sites of plasma membrane. It has been indicated that GABABR1 may not be transported to plasma membrane when no GABABR2 exists. Thus, it was presumed that GABABR1 in the cell body of the rat MTN neurons might not be involved in the synaptic transmission.}, author = {Li, Jin and Shigemoto, Ryuichi and Kulik, Ákos and Chen, Peng and Nomura, Sakashi and Kaneko, Takeshi and Mizuno, Noboru}, issn = {0304-3940}, journal = {Neuroscience Letters}, number = {1-2}, pages = {93 -- 97}, publisher = {Elsevier}, title = {{Immunocytochemical localization of GABAB receptors in mesencephalic trigeminal nucleus neurons in the rat}}, doi = {10.1016/S0304-3940(01)02321-7}, volume = {315}, year = {2001}, } @inbook{2709, author = {Erdös, László}, booktitle = {13th International Congress of Mathematical Physics}, isbn = {9781571460851}, pages = {273 -- 281}, publisher = { International Press of Boston}, title = {{Long time dynamics of an electron in a weakly coupled phonon field}}, year = {2001}, } @article{2610, abstract = {To study the role of mGlu7 receptors (mGluR7), we used homologous recombination to generate mice lacking this metabotropic receptor subtype (mGluR7 -/-). After the serendipitous discovery of a sensory stimulus-evoked epileptic phenotype, we tested two convulsant drugs, pentylenetetrazole (PTZ) and bicuculline. In animals aged 12 weeks and older, subthreshold doses of these drugs induced seizures in mGluR7 -/-, but not in mGluR7 +/-, mice. PTZ-induced seizures were inhibited by three standard anticonvulsant drugs, but not by the group III selective mGluR agonist (R,S)-4-phosphonophenylglycine (PPG). Consistent with the lack of signs of epileptic activity in the absence of specific stimuli, mGluR7 -/- mice showed no major changes in synaptic properties in two slice preparations. However, slightly increased excitability was evident in hippocampal slices. In addition, there was slower recovery from frequency facilitation in cortical slices, suggesting a role for mGluR7 as a frequency-dependent regulator in presynaptic terminals. Our findings suggest that mGluR7 receptors have a unique role in regulating neuronal excitability and that these receptors may be a novel target for the development of anticonvulsant drugs.}, author = {Sansig, Gilles and Bushell, Trevor and Clarke, Vernon and Rozov, Andrei and Burnashev, Nail and Portet, Chantal and Gasparini, Fabrizio and Schmutz, Markus and Klebs, Klaus and Shigemoto, Ryuichi and Flor, Peter and Kühn, Rainer and Knoepfel, Thomas and Schroeder, Markus and Hampson, David and Collett, Valerie and Zhang, Congxiao and Duvoisin, Robert and Collingridge, Graham and Van Der Putten, Herman}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {22}, pages = {8734 -- 8745}, publisher = {Society for Neuroscience}, title = {{Increased seizure susceptibility in mice lacking metabotropic glutamate receptor 7}}, doi = {10.1523/JNEUROSCI.21-22-08734.2001}, volume = {21}, year = {2001}, } @article{2609, abstract = {The metabotropic glutamate receptors (mGluRs) have distinct distribution patterns in the CNS but subtypes within group I or group III mGluRs share similar ultrastructural localization relative to neurotransmitter release sites: group I mGluRs are concentrated in an annulus surrounding the edge of the postsynaptic density, whereas group III mGluRs are concentrated in the presynaptic active zone. One of the group II subtypes, mGluR2, is expressed in both pre- and postsynaptic elements, having no close association with synapses. In order to determine if such a distribution is common to another group II subtype, mGluR3, an antibody was raised against a carboxy-terminus of mGluR3 and used for light and electron microscopic immunohistochemistry in the mouse CNS. The antibody reacted strongly with mGluR3, but it also reacted, though only weakly, with mGluR2. Therefore, to examine mGluR3-selective distribution, we used mGluR2-deficient mice as well as wild-type mice. Strong immunoreactivity for mGluR3 was found in the cerebral cortex, striatum, dentate gyrus of the hippocampus, olfactory tubercle, lateral septal nucleus, lateral and basolateral amygdaloid nuclei, and nucleus of the lateral olfactory tract. Pre-embedding immunoperoxidase and immunogold methods revealed mGluR3 labeling in both presynaptic and postsynaptic elements, and also in glial profiles. Double labeling revealed that the vast majority of mGluR3 in presynaptic elements is not closely associated with glutamate and GABA release sites in the striatum and thalamus, respectively. However, in the spines of the dentate granule cells, the highest receptor density was found in perisynaptic sites (20% of immunogold particles within 60 nm from the edge of postsynaptic membrane specialization) followed by a decreasing receptor density away from the synapses (to ∼5% of particles per 60 nm). Furthermore, 19% of immunogold particles were located in asymmetrical postsynaptic specialization, indicating an association of mGluR3 to glutamatergic synapses. The present results indicate that the localization of mGluR3 is rather similar to that of group I mGluRs in the postsynaptic elements, suggesting a unique functional role of mGluR3 in glutamatergic neurotransmission in the CNS.}, author = {Tamaru, Y and Nomura, Sakashi and Mizuno, Noboru and Shigemoto, Ryuichi}, issn = {0306-4522}, journal = {Neuroscience}, number = {3}, pages = {481 -- 503}, publisher = {Elsevier}, title = {{Distribution of metabotropic glutamate receptor mGluR3 in the mouse CNS: Differential location relative to pre- and postsynaptic sites}}, doi = {10.1016/S0306-4522(01)00305-0}, volume = {106}, year = {2001}, } @article{2608, abstract = {The regulation of neurotransmitter receptors during synapse formation has been studied extensively at the neuromuscular junction, but little is known about the development of excitatory neurotransmitter receptors during synaptogenesis in central synapses. In this study we show qualitatively and quantitatively that a receptor undergoes changes in localisation on the surface of rat Purkinje cells during development in association with its excitatory synapses. The presence of mGluR1α at parallel and climbing fibre synapses on developing Purkinje cells was studied using high-resolution immunoelectron microscopy. Immunoreactivity for mGluR1α was detected from embryonic day 18 in Purkinje cells, and showed dramatic changes in its localisation with age. At early postnatal ages (P0 and P3), mGluR1α was found both in somata and stem dendrites but was not usually associated with synaptic contacts. At P7, mGluR1α became concentrated in somatic spines associated with climbing fibres and in the growing dendritic arborisation even before innervation by parallel fibres. During the second and third postnatal week, when spines and parallel fibre synapses were generated, mGluR1α became progressively concentrated in the molecular layer, particularly in the synaptic specialisations. As a result, during the fourth postnatal week, the pattern and level of mGluR1α expression became similar to the adult and mGluR1α appeared in high density in perisynaptic sites. Our results indicate that mGluR1α is present in the developing Purkinje cells prior to their innervation by climbing and parallel fibres and demonstrate that this receptor undergoes a dynamic and specific regulation during postnatal development in association with the establishment of synaptic inputs to Purkinje cell.}, author = {López Bendito, Guillermina and Shigemoto, Ryuichi and Luján, Rafael and Juíz, José}, issn = {0306-4522}, journal = {Neuroscience}, number = {2}, pages = {413 -- 429}, publisher = {Elsevier}, title = {{Developmental changes in the localisation of the mGluR1α subtype of metabotropic glutamate receptors in Purkinje cells}}, doi = {10.1016/S0306-4522(01)00188-9}, volume = {105}, year = {2001}, } @article{2607, abstract = {Alternative splicing in the mGluR5 gene generates two different receptor isoforms, of which expression is developmentally regulated. However, little is known about the functional significance of mGluR5 splice variants. We have examined the functional coupling, subcellular targeting, and effect on neuronal differentiation of epitope-tagged mGluR5 isoforms by expression in neuroblastoma NG108-15 cells. We found that both mGluR5 splice variants give rise to comparable [Ca2+]i transients and have similar pharmacological profile. Tagged receptors were shown by immunofluorescence to be inserted in the plasma membrane. In undifferentiated cells the subcellular localization of the two mGluR5 isoforms was partially segregated, whereas in differentiated cells the labeling largely redistributed to the newly formed neurites. Interestingly, we demonstrate that mGluR5 splice variants dramatically influence the formation and maturation of neurites; mGluR5a hinders the acquisition of mature neuronal traits and mGluR5b fosters the elaboration and extension of neurites. These effects are partly inhibited by MPEP.}, author = {Mion, Silvia and Corti, Corrado and Neki, Akio and Shigemoto, Ryuichi and Corsi, Mauro and Fumagalli, Guido and Ferraguti, Francesco}, issn = {1044-7431}, journal = {Molecular and Cellular Neuroscience}, number = {6}, pages = {957 -- 972}, publisher = {Academic Press}, title = {{Bidirectional regulation of neurite elaboration by alternatively spliced metabotropic glutamate receptor 5 (mGluR5) isoforms}}, doi = {10.1006/mcne.2001.0993}, volume = {17}, year = {2001}, } @article{2605, abstract = {The granular layer of the cerebellar cortex consists of densely packed neuronal cells, classified into granule cells and large interneurons. In this study, we provide a comparative survey of large granular layer interneurons in the adult rat cerebellum based on both morphological and neurochemical criteria. To this end, double immunofluorescence histochemistry was performed by combining antibodies against the cytoplasmic antigen Rat-303, calretinin, the metabotropic glutamate receptor mGluR2 and somatostatin. Based on Rat-303/calretinin double immunohistochemistry, three distinct populations of large granular layer interneurons could be discerned: cells immunopositive for Rat-303, calretinin or both. Rat-303 or calretinin single-labeled cells represented Golgi cells and unipolar brush cells, respectively. Rat-303/calretinin double-labeled cells located just underneath the Purkinje cell layer represented Lugaro cells. Morphometrical analysis distinguished two populations of Rat-303-positive Golgi cells according to their location: vermis versus hemisphere. Immunostaining for the metabotropic glutamate receptor mGluR2 combined with Rat-303 or calretinin revealed that the majority of Golgi cells (about 90%) appeared to be mGluR2 positive. Lugaro cells were mGluR2 negative. In addition, a limited population of large polymorphous interneurons in the depth of the granular layer with morphological features resembling Golgi cells also displayed Rat-303/calretinin immunoreactivity and were mGluR2 negative. Double immunohistochemistry for Rat-303 and somatostatin revealed three populations of labeled cells in the depth of the granular layer. Besides double-labeled Golgi cells, Rat-303 or somatostatin single-labeled cells were present. Based on mGluR2/somatostatin and calretinin/somatostatin double immunostainings, Rat-303 single-labeled cells were found to correspond to Rat-303/calretinin-positive, mGluR2-negative Golgi-like cells, while the identity of somatostatin single-labeled cells remained unclear. The data presented in this article elaborate previous reports on the morphological and neurochemical differentiation of large interneurons in the rat cerebellar granular layer. In addition, they indicate that the current classification of these cells into Golgi cells, Lugaro cells and unipolar brush cells does not describe the observed neurochemical heterogeneity.}, author = {Geurts, Frederik and Timmermans, Jean and Shigemoto, Ryuichi and De Schutter, Erik}, issn = {0306-4522}, journal = {Neuroscience}, number = {2}, pages = {499 -- 512}, publisher = {Elsevier}, title = {{Morphological and neurochemical differentiation of large granular layer interneurons in the adult rat cerebellum}}, doi = {10.1016/S0306-4522(01)00058-6}, volume = {104}, year = {2001}, } @article{2604, abstract = {Cutaneous antidromic vasodilatation and plasma extravasation, two phenomena that occur in neurogenic inflammation, are partially blocked by substance P (SP) receptor antagonists and are known to be mediated in part by mast cell-released substances, such as histamine, serotonin, and nitric oxide. In an attempt to provide a morphological substrate for the above phenomena, we applied light and electron microscopic immunocytochemistry to investigate the pattern of SP innervation of blood vessels and its relationship to mast cells in the skin of the rat lower lip. Furthermore, we examined the distribution of SP (neurokinin-1) receptors and their relationship to SP-immunoreactive (IR) fibers. Our results confirmed that SP-IR fibers are found in cutaneous nerves and that terminal branches are observed around blood vessels and penetrating the epidermis. SP-IR fibers also innervated hair follicles and sebaceous glands. At the ultrastructural level, SP-IR varicosities were observed adjacent to arterioles, capillaries, venules, and mast cells. The varicosities possessed both dense core vesicles and agranular synaptic vesicles. We quantified the distance between SP-IR varicosities and blood vessel endothelial cells. SP-IR terminals were located within 0.23-5.99 μm from the endothelial cell layer in 82.7% of arterioles, in 90.2% of capillaries, and in 86.9% of venules. Although there was a trend for SP-IR fibers to be located closer to the endothelium of venules, this difference was not significant. Neurokinin-1 receptor (NK-1r) immunoreactivity was most abundant in the upper dermis and was associated with the wall of blood vessels. NK-1r were located in equal amounts on the walls of arterioles, capillaries, and venules that were innervated by SP-IR fibers. The present results favor the concept of a participation of SP in cutaneous neurogenic vasodilatation and plasma extravasation both by an action on blood vessels after binding to the NK-1r and by causing the release of substances from mast cells after diffusion through the connective tissue.}, author = {Ruocco, Isabella and Cuello, Augusto and Shigemoto, Ryuichi and Ribeiro Da Silva, Alfredo}, issn = {0021-9967}, journal = {Journal of Comparative Neurology}, number = {4}, pages = {466 -- 480}, publisher = {Wiley-Blackwell}, title = {{Light and electron microscopic study of the distribution of substance P-immunoreactive fibers and neurokinin-1 receptors in the skin of the rat lower lip}}, doi = {10.1002/cne.1114}, volume = {432}, year = {2001}, } @article{2606, abstract = {Glutamate receptors have been linked to the regulation of several developmental events in the CNS. By using cortical slices of early postnatal mice, we show that in layer I cells, glutamate produces intracellular calcium ([Ca2+]i) elevations mediated by ionotropic and metabotropic glutamate receptors (mGluRs). The contribution of mGluRs to these responses was demonstrated by application of tACPD, an agonist to groups I and II mGluRs, which evoked [Ca2+]i increases that could be reversibly blocked by MCPG, an antagonist to groups I and II mGluRs. In the absence of extracellular Ca2+, repetitive applications of tACPD or quisqualate, an agonist to group I mGluRs, elicited decreasing [Ca2+]i responses that were restored by refilling a thapsigargin-sensitive Ca2+ store. The use of specific group I mGluR agonists CHPG and DHPG indicated that the functional mGluR in layer I was of the mGluR1 subtype. Subtype specific antibodies confirmed the presence of mGlur1α, but not mGluR5, in Cajal-Retzius (Reelin-immunoreactive) neurons.}, author = {Martínez, Galán and López Bendito, Guillermina and Luján, Rafael and Shigemoto, Ryuichi and Fairén, Alfonso and Valdeolmillos, Miguel}, issn = {0953-816X}, journal = {European Journal of Neuroscience}, number = {6}, pages = {1147 -- 1154}, publisher = {Wiley-Blackwell}, title = {{Cajal-Retzius cells in early postnatal mouse cortex selectively express functional metabotropic glutamate receptors}}, doi = {10.1046/j.0953-816X.2001.01494.x}, volume = {13}, 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}, } @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{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{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{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{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}, } @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{1452, abstract = {In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system.}, author = {Hausel, Tamas and Thaddeus, Michael}, issn = {0764-4442}, journal = {Comptes Rendus de l'Academie des Sciences - Series I: Mathematics}, number = {4}, pages = {313 -- 318}, publisher = {Elsevier}, title = {{Examples of mirror partners arising from integrable systems}}, doi = {10.1016/S0764-4442(01)02057-2}, volume = {333}, 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}, } @article{1453, abstract = {In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0370-2693}, journal = {Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics}, number = {1-2}, pages = {189 -- 199}, publisher = {Elsevier}, title = {{Geometric construction of new Yang-Mills instantons over Taub-NUT space}}, doi = {10.1016/S0370-2693(01)00821-8}, volume = {514}, year = {2001}, } @article{1454, abstract = {We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0393-0440}, journal = {Journal of Geometry and Physics}, number = {1-2}, pages = {126 -- 136}, publisher = {Elsevier}, title = {{Geometric interpretation of Schwarzschild instantons}}, doi = {10.1016/S0393-0440(00)00040-1}, volume = {37}, 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{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{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{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{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{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}, }