@article{1797, abstract = {Intrinsically photosensitive melanopsin-containing retinal ganglion cells (ipRGCs) control important physiological processes, including the circadian rhythm, the pupillary reflex, and the suppression of locomotor behavior (reviewed in [1]). ipRGCs are also activated by classical photoreceptors, the rods and cones, through local retinal circuits [2, 3]. ipRGCs can be transsynaptically labeled through the pupillary-reflex circuit with the derivatives of the Bartha strain of the alphaherpesvirus pseudorabies virus(PRV) [4, 5] that express GFP [6-12]. Bartha-strain derivatives spread only in the retrograde direction [13]. There is evidence that infected cells function normally for a while during GFP expression [7]. Here we combine transsynaptic PRV labeling, two-photon laser microscopy, and electrophysiological techniques to trace the local circuit of different ipRGC subtypes in the mouse retina and record light-evoked activity from the transsynaptically labeled ganglion cells. First, we show that ipRGCs are connected by monostratified amacrine cells that provide strong inhibition from classical-photoreceptor-driven circuits. Second, we show evidence that dopaminergic interplexiform cells are synaptically connected to ipRGCs. The latter finding provides a circuitry link between light-dark adaptation and ipRGC function.}, author = {Viney, Tim J and Bálint, Kamill and Hillier, Dániel and Sandra Siegert and Boldogköi, Zsolt S and Enquist, Lynn W and Meister, Markus and Cepko, Constance L and Roska, Botond M}, journal = {Current Biology}, number = {11}, pages = {981 -- 988}, publisher = {Cell Press}, title = {{Local retinal circuits of melanopsin-containing ganglion cells identified by transsynaptic viral tracing}}, doi = {10.1016/j.cub.2007.04.058}, volume = {17}, year = {2007}, } @article{18035, abstract = {We compare the low bias conductance of a series of alkanes terminated on their ends with dimethyl phosphines, methyl sulfides, and amines and find that junctions formed with dimethyl phosphine terminated alkanes have the highest conductance. We see unambiguous conductance signatures with these link groups, indicating that the binding is well-defined and electronically selective. This allows a detailed analysis of the single-molecule junction elongation properties which correlate well with calculations based on density functional theory.}, author = {Park, Young S. and Whalley, Adam C. and Kamenetska, Maria and Steigerwald, Michael L. and Hybertsen, Mark S. and Nuckolls, Colin and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {51}, pages = {15768--15769}, publisher = {American Chemical Society}, title = {{Contact chemistry and single-molecule conductance:  A comparison of phosphines, methyl sulfides, and amines}}, doi = {10.1021/ja0773857}, volume = {129}, year = {2007}, } @article{18036, abstract = {We measured conductance traces while breaking gold point contacts in a solution of molecules containing the μ-p-phenylenediethynyl X−C⋮C−C6H4−C⋮C−X unit, with eight different capping X groups:  Au−P(OMe)3 (1), H (2), SiMe3 (3), Au−P(cy)3 (4), Au−PMe2Ph (5), Au−PMePh2 (6), Au−PMe3 (7), and Au−PPh3 (8). Our goal with this work was to achieve a direct Au−C link with a conjugated organic group, potentially forming a molecular junction without chemical link groups that typically decrease junction conductances, such as thiols or amines. Conductance traces collected in the presence of molecules 1, 2, 3, 5, and 7 reveal additional steps at conductances as high as 0.1 G0 (G0 = 2e2/h) down to the measurable limits of the experimental setup. Conductance histograms generated from these traces therefore show a broad increase of counts when compared to a control histogram collected in the solvent alone suggesting the binding of the molecules to the broken Au contacts. The histograms for molecules 1, 5, 7, and 2 were not distinguishable, although that of molecule 3 had considerably fewer counts over the entire conductance range, suggesting that the steric bulk of the SiMe3 prevented frequent junction formation. The histograms collected in a solution of molecules 4, 6, or 8 did not differ from that of the control histogram probably because of the steric bulk of the Au−PR3 capping groups prevented the formation a molecular junction.}, author = {Millar, David and Venkataraman, Latha and Doerrer, Linda H.}, issn = {1932-7455}, journal = {The Journal of Physical Chemistry C}, number = {47}, pages = {17635--17639}, publisher = {American Chemical Society}, title = {{Efficacy of Au−Au contacts for scanning tunneling microscopy molecular conductance measurements}}, doi = {10.1021/jp0756101}, volume = {111}, year = {2007}, } @article{18037, abstract = {A combination of theory and experiment is used to quantitatively understand the conductance of single-molecule benzenediamine−gold junctions. A newly developed analysis is applied to a measured junction conductance distribution, based on 59 000 individual conductance traces, which has a clear peak at 0.0064 G0 and a width of ±47%. This analysis establishes that the distribution width originates predominantly from variations in conductance across different junctions rather than variations in conductance during junction elongation. Conductance calculations based on density functional theory (DFT) for 15 distinct junction geometries show a similar spread. We show explicitly that differences in local structure have a limited influence on conductance because the amine−Au bonding motif is well-defined and flexible, explaining the narrow distributions seen in the experiments. The minimal impact of junction structure on conductance permits an unambiguous comparison of calculated and measured conductance values and a direct assessment of the widely used DFT theoretical framework. The average calculated conductance (0.046 G0) is found to be seven times larger than experiment. This discrepancy is explained quantitatively in terms of electron correlation effects to the molecular level alignments in the junction.}, author = {Quek, Su Ying and Venkataraman, Latha and Choi, Hyoung Joon and Louie, Steven G. and Hybertsen, Mark S. and Neaton, J. B.}, issn = {1530-6992}, journal = {Nano Letters}, number = {11}, pages = {3477--3482}, publisher = {American Chemical Society}, title = {{Amine−gold linked single-molecule circuits:  Experiment and theory}}, doi = {10.1021/nl072058i}, volume = {7}, year = {2007}, } @article{18038, abstract = {Cyclic voltammetry determines first and second oxidation potentials of conducting diamines. The results show that unsubstituted and methyl-substituted molecules conduct electricity in partially positively charged states, reflecting electron delocalization at the wire−gold junctions, but with electron-withdrawing substituents, the molecular wires are closer to uncharged as conductors, consistent with HOMO arguments.}, author = {Quinn, Jordan R. and Foss, Frank W. and Venkataraman, Latha and Breslow, Ronald}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {41}, pages = {12376--12377}, publisher = {American Chemical Society}, title = {{Oxidation potentials correlate with conductivities of aromatic molecular wires}}, doi = {10.1021/ja0745097}, volume = {129}, year = {2007}, } @article{18039, abstract = {Conductivities have been measured for diaminoacenes with benzene, naphthalene, and anthracene rings. The conductivities were strong functions of the placement of the amino group contact points for the gold electrodes. There was good correlation with quantum-mechanical theory, and with the stabilities of the related mono- and dications of the molecules. It is proposed that some electron abstraction by the drain precedes electron donation by the source with these electron-rich systems.}, author = {Quinn, Jordan R. and Foss, Frank W. and Venkataraman, Latha and Hybertsen, Mark S. and Breslow, Ronald}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {21}, pages = {6714--6715}, publisher = {American Chemical Society}, title = {{Single-molecule junction conductance through diaminoacenes}}, doi = {10.1021/ja0715804}, volume = {129}, year = {2007}, } @article{18040, abstract = {We measure the low bias conductance of a series of substituted benzene diamine molecules while breaking a gold point contact in a solution of the molecules. Transport through these substituted benzenes is by means of nonresonant tunneling or superexchange, with the molecular junction conductance depending on the alignment of the metal Fermi level to the closest molecular level. Electron-donating substituents, which drive the occupied molecular orbitals up, increase the junction conductance, while electron-withdrawing substituents have the opposite effect. Thus for the measured series, conductance varies inversely with the calculated ionization potential of the molecules. These results reveal that the occupied states are closest to the gold Fermi energy, indicating that the tunneling transport through these molecules is analogous to hole tunneling through an insulating film.}, author = {Venkataraman, Latha and Park, Young S. and Whalley, Adam C. and Nuckolls, Colin and Hybertsen, Mark S. and Steigerwald, Michael L.}, issn = {1530-6992}, journal = {Nano Letters}, number = {2}, pages = {502--506}, publisher = {American Chemical Society}, title = {{Electronics and dhemistry:  Varying single-molecule junction conductance using chemical substituents}}, doi = {10.1021/nl062923j}, volume = {7}, year = {2007}, } @inproceedings{18336, abstract = {In this paper, we address the problem of partial comparison of non-rigid objects. We introduce a new class of set-valued distances, related to the concept of Pareto optimality in economics. Such distances allow to capture intrinsic geometric similarity between parts of non-rigid objects, obtaining semantically meaningful comparison results. The numerical implementation of our method is computationally efficient and is similar to GMDS, a multidimensional scaling-like continuous optimization problem.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Bruckstein, Alfred M. and Kimmel, Ron}, booktitle = {First International Conference on Scale Space and Variational Methods in Computer Vision}, isbn = {9783540728221}, location = {Ischia, Italy}, pages = {264--275}, publisher = {Springer Nature}, title = {{Paretian similarity for partial comparison of non-rigid objects}}, doi = {10.1007/978-3-540-72823-8_23}, volume = {4485}, year = {2007}, } @article{18367, abstract = {We propose an efficient computational solver for eikonal equations on parametric three-dimensional manifolds. Our approach is based on the fast marching method for solving the eikonal equation in ð(n log n) steps on n grid points by numerically simulating wavefront propagation. The obtuse angle splitting problem is reformulated as a set of small integer linear programs, that can be solved in ð(n). Numerical simulations demonstrate the accuracy of the proposed algorithm.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, issn = {0021-9991}, journal = {Journal of Computational Physics}, number = {1}, pages = {771--784}, publisher = {Elsevier}, title = {{Weighted distance maps computation on parametric three-dimensional manifolds}}, doi = {10.1016/j.jcp.2007.01.009}, volume = {225}, year = {2007}, } @inproceedings{18389, abstract = {This paper explores similarity criteria between non-rigid shapes. Broadly speaking, such criteria are divided into intrinsic and extrinsic, the first referring to the metric structure of the objects and the latter to the geometry of the shapes in the Euclidean space. Both criteria have their advantages and disadvantages; extrinsic similarity is sensitive to non-rigid deformations of the shapes, while intrinsic similarity is sensitive to topological noise. Here, we present an approach unifying both criteria in a single distance. Numerical results demonstrate the robustness of our approach in cases where using only extrinsic or intrinsic criteria fail.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, booktitle = {11th International Conference on Computer Vision}, isbn = {9781424416301}, issn = {1550-5499}, location = {Rio de Janeiro, Brazil}, publisher = {IEEE}, title = {{Rock, paper, and scissors: Extrinsic vs. intrinsic similarity of non-rigid shapes}}, doi = {10.1109/iccv.2007.4409076}, year = {2007}, } @inproceedings{18390, abstract = {Symmetry and self-similarity is the cornerstone of Nature, exhibiting itself through the shapes of natural creations and ubiquitous laws of physics. Since many natural objects are symmetric, the absence of symmetry can often be an indication of some anomaly or abnormal behavior. Therefore, detection of asymmetries is important in numerous practical applications, including crystallography, medical imaging, and face recognition, to mention a few. Conversely, the assumption of underlying shape symmetry can facilitate solutions to many problems in shape reconstruction and analysis. Traditionally, symmetries are described as extrinsic geometric properties of the shape. While being adequate for rigid shapes, such a description is inappropriate for non-rigid ones. Extrinsic symmetry can be broken as a result of shape deformations, while its intrinsic symmetry is preserved. In this paper, we pose the problem of finding intrinsic symmetries of non-rigid shapes and propose an efficient method for their computation.}, author = {Raviv, Dan and Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, booktitle = {11th International Conference on Computer Vision}, isbn = {9781424416301}, issn = {2380-7504}, location = {Rio de Janeiro, Brazil}, publisher = {IEEE}, title = {{Symmetries of non-rigid shapes}}, doi = {10.1109/iccv.2007.4409181}, volume = {72}, year = {2007}, } @article{18420, abstract = {The experience of motion sickness in a virtual environment may be measured through pre and postexperiment self-reported questionnaires such as the simulator sickness questionnaire (SSQ). Although research provides converging evidence that users of virtual environments can experience motion sickness, there have been no controlled studies to determine to what extent the user's subjective response is a demand characteristic resulting from pre and posttest measures. In this study, subjects were given either SSQ's both pre and postvirtual environment immersion, or only postimmersion. This technique tested for contrast effects due to demand characteristics in which administration of the questionnaire itself suggested to the participant that the virtual environment may produce motion sickness. Results indicate that reports of motion sickness after immersion in a virtual environment are much greater when both pre and postquestionnaires are given than when only a posttest questionnaire is used. The implications for assessments of motion sickness in virtual environments are discussed}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, issn = {1941-0506}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {5}, pages = {902--913}, publisher = {IEEE}, title = {{Calculus of nonrigid surfaces for geometry and texture manipulation}}, doi = {10.1109/tvcg.2007.1041}, volume = {13}, year = {2007}, } @article{128, abstract = {A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. }, author = {Carr, Adra and Serchest, Yancey and Waitukaitis, Scott R and Perreault, John and Lonij, Vincent and Cronin, Alexander}, journal = {Review of Scientific Instruments}, number = {10}, publisher = {American Institute of Physics}, title = {{Cover slip external cavity diode laser}}, doi = {10.1063/1.2801006}, volume = {78}, year = {2007}, } @article{1297, abstract = {In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species.}, author = {Raghu, Shamprasad V and Maximilian Jösch and Borst, Alexander and Reiff, Dierk F}, journal = {Journal of Comparative Neurology}, number = {4}, pages = {598 -- 610}, publisher = {Wiley-Blackwell}, title = {{Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites}}, doi = {10.1002/cne.21319}, volume = {502}, year = {2007}, } @article{1964, abstract = {Complex I of respiratory chains plays a central role in cellular energy production. Mutations in its subunits lead to many human neurodegenerative diseases. Recently, a first atomic structure of the hydrophilic domain of complex I from Thermus thermophilus was determined. This domain represents a catalytic core of the enzyme. It consists of eight different subunits, contains all the redox centers, and comprises more than half of the entire complex. In this review, novel mechanistic implications of the structure are discussed, and the effects of many known mutations of complex I subunits are interpreted in a structural context.}, author = {Leonid Sazanov}, journal = {Biochemistry}, number = {9}, pages = {2275 -- 2288}, publisher = {ACS}, title = {{Respiratory complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain}}, doi = {10.1021/bi602508x}, volume = {46}, year = {2007}, } @article{1965, abstract = {Respiratory complex I (NADH:ubiquinone oxidoreductase) is an L-shaped multisubunit protein assembly consisting of a hydrophobic membrane arm and a hydrophilic peripheral arm. It catalyses the transfer of two electrons from NADH to quinone coupled to the translocation of four protons across the membrane. Although we have solved recently the crystal structure of the peripheral arm, the structure of the complete enzyme and the coupling mechanism are not yet known. The membrane domain of Escherichia coli complex I consists of seven different subunits with total molecular mass of 258 kDa. It is significantly more stable than the whole enzyme, which allowed us to obtain well-ordered two-dimensional crystals of the domain, belonging to the space group p22121. Comparison of the projection map of negatively stained crystals with previously published low-resolution structures indicated that the characteristic curved shape of the membrane domain is remarkably well conserved between bacterial and mitochondrial enzymes, helping us to interpret projection maps in the context of the intact complex. Two pronounced stain-excluding densities at the distal end of the membrane domain are likely to represent the two large antiporter-like subunits NuoL and NuoM. Cryo-electron microscopy on frozen-hydrated crystals allowed us to calculate a projection map at 8 Å resolution. About 60 transmembrane α-helices, both perpendicular to the membrane plane and tilted, are present within one membrane domain, which is consistent with secondary structure predictions. A possible binding site and access channel for quinone are found at the interface with the peripheral arm. Tentative assignment of individual subunits to the features of the map has been made. The location of subunits NuoL and NuoM at substantial distance from the peripheral arm, which contains all the redox centres of the complex, indicates that conformational changes are likely to play a role in the mechanism of coupling between electron transfer and proton pumping.}, author = {Baranova, Ekaterina A and Holt, Peter J and Leonid Sazanov}, journal = {Journal of Molecular Biology}, number = {1}, pages = {140 -- 154}, publisher = {Elsevier}, title = {{Projection structure of the membrane domain of Escherichia coli respiratory Complex I at 8 Å resolution}}, doi = {10.1016/j.jmb.2006.11.026}, volume = {366}, year = {2007}, } @article{1969, abstract = {Respiratory complex I catalyses the transfer of electrons from NADH to quinone coupled to the translocation of protons across the membrane. The mechanism of coupling and the structure of the complete enzyme are not known. The membrane domain of the complex contains three similar antiporter-like subunits NuoL/M/N, probably involved in proton pumping. We have previously shown that subunits NuoL/M can be removed from the rest of the complex, suggesting their location at the distal end of the membrane domain. Here, using electron microscopy and single particle analysis, we show that subunits NuoL and M jointly occupy a distal half of the membrane domain, separated by about 10 nm from the interface with the peripheral arm. This indicates that coupling mechanism of complex I is likely to involve long range conformational changes.}, author = {Baranova, Ekaterina A and Morgan, David J and Leonid Sazanov}, journal = {Journal of Structural Biology}, number = {2 SPEC. ISS.}, pages = {238 -- 242}, publisher = {Academic Press}, title = {{Single particle analysis confirms distal location of subunits NuoL and NuoM in Escherichia coli complex I}}, doi = {10.1016/j.jsb.2007.01.009}, volume = {159}, year = {2007}, } @article{11115, abstract = {The formation of the nuclear envelope (NE) around chromatin is a major membrane-remodelling event that occurs during cell division of metazoa. It is unclear whether the nuclear membrane reforms by the fusion of NE fragments or if it re-emerges from an intact tubular network of the endoplasmic reticulum (ER). Here, we show that NE formation and expansion requires a tubular ER network and occurs efficiently in the presence of the membrane fusion inhibitor GTPγS. Chromatin recruitment of membranes, which is initiated by tubule-end binding, followed by the formation, expansion and sealing of flat membrane sheets, is mediated by DNA-binding proteins residing in the ER. Thus, chromatin plays an active role in reshaping of the ER during NE formation.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1476-4679}, journal = {Nature Cell Biology}, keywords = {Cell Biology}, number = {10}, pages = {1160--1166}, publisher = {Springer Nature}, title = {{Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum}}, doi = {10.1038/ncb1636}, volume = {9}, year = {2007}, } @article{11116, abstract = {The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107–160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107–160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.}, author = {Franz, Cerstin and Walczak, Rudolf and Yavuz, Sevil and Santarella, Rachel and Gentzel, Marc and Askjaer, Peter and Galy, Vincent and HETZER, Martin W and Mattaj, Iain W and Antonin, Wolfram}, issn = {1469-3178}, journal = {EMBO reports}, keywords = {Genetics, Molecular Biology, Biochemistry}, number = {2}, pages = {165--172}, publisher = {EMBO}, title = {{MEL‐28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly}}, doi = {10.1038/sj.embor.7400889}, volume = {8}, year = {2007}, } @article{1035, abstract = {We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character.}, author = {Mark, Michael and Ferlaino, Francesca and Knoop, Steven and Danzl, Johann G and Kraemer, Tobias and Chin, Cheng and Nägerl, Hanns and Grimm, Rudolf}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Spectroscopy of ultracold trapped cesium Feshbach molecules}}, doi = {10.1103/PhysRevA.76.042514}, volume = {76}, year = {2007}, }