Comparison of the experimental, semi-experimental and ab initio equilibrium structures of acetylene: Influence of relativisitic effects and of the diagonal Born-Oppenheimer corrections

The equilibrium structure of acetylene (also named ethyne) has been reinvestigated to resolve the small discrepancies noted between different determinations. The size of the system as well as the large amount of available experimental data provides the quite unique opportunity to check the magnitude and relevance of various contributions to equilibrium structure as well as to verify the accuracy of experimental results. With respect to pure theoretical investigation, quantum-chemical calculations at the coupled-cluster level have been employed together with extrapolation to the basis set limit, consideration of higher excitations in the cluster operator, inclusion of core correlation effects as well as relativistic and diagonal Born-Oppenheimer corrections. In particular, it is found that the extrapolation to the complete basis set limit, the inclusion of higher excitations in the electronic-correlation treatment and the relativistic corrections are of the same order of magnitude. It also appears that a basis set as large as a core-valence quintuple-zeta set is required for accurately accounting for the inner-shell correlation contribution. From a pure experimental point of view, the equilibrium structure has been determined using very accurate rotational constants recently obtained by a global analysis (that is to say that all non-negligible interactions are explicitely included in the Hamiltonian matrix) of rovibrational spectra. Finally, a semi-experimental equilibrium structure (where the equilibrium rotational constants are obtained from the experimental ground state rotational constants and computed rovibrational corrections) has been obtained from the available experimental ground-state rotational constants for ten isotopic species corrected for computed vibrational corrections. Such a determination led to the revision of the ground-state rotational constants of two isotopologues, thus showing that structural determination is a good method to identify errors in experimental rotational constants. The three structures are found in a very good agreement, and our recommended values are rCC 120.2958(7) pm and rCH 106.164(1) pm. © 2011 American Institute of Physics.

Dramatic structure in the photodetachment of inner shells of negative ions: Li-

Deep inner-shell photodetachment of negative ions is shown to differ qualitatively and quantitatively from the corresponding process in neutral atoms and positive ions. As an example, calculations of the photodetachment of Li- out of the 1s shell, using an augmented R-matrix methodology, are presented and show numerous structures over a broad energy region including a new phenomenon: Auger decay of a shape resonance. Li- was selected because it is the simplest multishell negative ion and is amenable to experimental scrutiny.

A numerical investigation of the flow structures and losses for turbulent flow in 90 degrees elbow bends

Computational fluid dynamic modelling was carried out on a series of pipe bends having R/r values of 1.3, 5, and 20, with the purpose of determining the accuracy of numerical models in predicting pressure loss data from which to inform one-dimensional loss models. Four separate turbulence models were studied: the standard k-epsilon model, realizable k-epsilon model, k-omega model, and a Reynolds stress model (RSM). The results are presented for each bend in the form of upstream and downstream pressure profiles, pressure distributions along the inner and outer walls, detailed pressure and velocity fields as well as overall loss values. In each case, measured data were presented to evaluate the predictive ability of each model. The RSM was found to perform the best, producing accurate pressure loss data for bends with R/r values of 5 and 20. For the tightest bend with an R/r value of 1.3, however, predictions were significantly worse due to the presence of flow separation, stronger pressure gradients, and high streamline curvature.

The social consequences of broken urban structures: a case study of Belfast

This article explores how the design and layout of the urban environment can have significant social impacts on working class communities whose access to employment and other necessary services depends largely on public transport and safe walk-able streets. It does so by considering a case study of Belfast. Although Belfast has a distinctive recent history as the site of political violence and territorial division, it also has a spatial configuration that emerged out of a modernising roads and redevelopment programme in the 1960s and 1970s. However, an understanding of contemporary Belfast, particularly its urban structure and form, requires n analysis of how the social impacts of such ubiquitous regional and urban planning practices were not addressed. The article argues that a culture of ‘politically safe’ bureaucratic inaction developed during the ‘war years’ has been sustained in the ‘new democracy’. In turn, this has had significant consequences for the functioning of the city. Major areas of derelict land around the city core together with the impediments created by regional road infrastructure have combined to create a doughnut city that, on the one hand, facilitates a commuting middle class, while on the other, discriminates against the poorest inner city communities. The article goes on to examine how an activist urban design group, known as the Forum for Alternative Belfast, has responded to these challenges. It focuses particularly on action-research undertaken during its 2010 Summer School which aimed to address issues of disconnection in inner North Belfast that affect some of the most territorialised and deprived communities in the city.

Free-breathing inner-volume black-blood imaging of the human heart using two-dimensionally selective local excitation at 3 T.

Black-blood fast spin-echo imaging is a powerful technique for the evaluation of cardiac anatomy. To avoid fold-over artifacts, using a sufficiently large field of view in phase-encoding direction is mandatory. The related oversampling affects scanning time and respiratory chest motion artifacts are commonly observed. The excitation of a volume that exclusively includes the heart without its surrounding structures may help to improve scan efficiency and minimize motion artifacts. Therefore, and by building on previously reported inner-volume approach, the combination of a black-blood fast spin-echo sequence with a two-dimensionally selective radiofrequency pulse is proposed for selective "local excitation" small field of view imaging of the heart. This local excitation technique has been developed, implemented, and tested in phantoms and in vivo. With this method, small field of view imaging of a user-specified region in the human thorax is feasible, scanning becomes more time efficient, motion artifacts can be minimized, and additional flexibility in the choice of imaging parameters can be exploited.

The effect of Nystatin on the inner ear : an experimental guinea pig study

Objectifs: Le Nystatin est un antibiotique efficace pour le traitement d’otomycose. Bien que sa sécurité au niveau de l’oreille externe soit bien établie, son utilisation n’est pas recommandée lorsqu’il y a une perforation tympanique. L’objectif de cette étude est d’évaluer le potentiel ototoxique du Nystatin lorsque celui-ci est appliqué directement au niveau de l’oreille moyenne. Méthodes: Nous avons fait une étude expérimentale avec 18 cochons d’Indes de souche Hartley que nous avons divisés en deux groupes. En exposant l’oreille moyenne de chaque animal au Nystatin (groupe I) ou à la néomycine (groupe II) et chaque oreille controlatérale à une solution physiologique (NaCl), la fonction auditive a été évaluée avec un test de potentiels évoqués auditif du tronc cérébral avant et après les injections. Une étude par microscopie électronique a permis une comparaison histologique de l’état des cellules ciliées cochléaires entre les 2 groupes. Résultats: Les pertes auditives moyennes du groupe « Nystatin » étaient de 13.0 dB et comparables aux pertes moyennes observées dans les oreilles ayant été injectées avec du NaCl (4.0 dB dans le groupe I et 15.1 dB dans le groupe II). Le groupe de contrôle « néomycine » a subi une perte auditive moyenne de 39.3 dB, ce qui représente une différence cliniquement et statistiquement significative (p<0.001). L’étude histologique avec une microscopie à balayage électronique a démontré une conservation de l’architecture des cellules ciliées cochléaires dans les groupe Nystatin et NaCl. La néomycine a causé une destruction marquée de ces structures. Conclusions: Le Nystatin ne provoque pas d’atteinte auditive ni de destruction des cellules ciliées externes après injection directe dans l’oreille moyenne chez le cochon d’Inde.

Conformal structures and twistors in the paravector model of spacetime

Some properties of the Clifford algebras Cl-3,Cl-0, Cl-1,Cl-3, Cl-4,Cl-1 similar or equal to C circle times Cl-1,Cl-3 and Cl-2,Cl-4 are presented, and three isomorphisms between the Dirac-Clifford algebra C circle times Cl-1,Cl-3 and Cl-4,Cl-1 are exhibited, in order to construct conformal maps and twistors, using the paravector model of spacetime. The isomorphism between the twistor space inner product isometry group SU( 2,2) and the group $pin(+)(2,4) is also investigated, in the light of a suitable isomorphism between C circle times Cl-1,Cl-3 and Cl-4,Cl-1. After reviewing the conformal spacetime structure, conformal maps are described in Minkowski spacetime as the twisted adjoint representation of $ pin(+)(2,4), acting on paravectors. Twistors are then presented via the paravector model of Clifford algebras and related to conformal maps in the Clifford algebra over the Lorentzian R-4,(1) spacetime.We construct twistors in Minkowski spacetime as algebraic spinors associated with the Dirac-Clifford algebra C circle times Cl-1,Cl-3 using one lower spacetime dimension than standard Clifford algebra formulations, since for this purpose, the Clifford algebra over R-4,R-1 is also used to describe conformal maps, instead of R-2,(4). Our formalism sheds some new light on the use of the paravector model and generalizations.

Integrability vs supersymmetry: Poisson structures of the pohlmeyer reduction

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin

Both human and bovine prothrombin fragment 2 (the second kringle) have been cocrystallized separately with human PPACK (D-Phe-Pro-Arg)-thrombin, and the structures of these noncovalent complexes have been determined and refined (R = 0.155 and 0.157, respectively) at 3.3-Å resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogens K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg70Asp substitution, but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix, and the hairpin β-turn of the second inner loop pivots at Val64 and Asp70 by 60°. Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating any vestige of the cationic center of the lysine binding site. Since fragment 2 has not been reported to bind lysine, it most likely has a different inherent folding conformation for the second outer loop, as has also been observed to be the case with TPA K2 and the urokinase kringle. The movement of the Val64-Asp70 β-turn is most likely a conformational change accompanying complexation, which reveals a new heretofore unsuspected flexibility in kringles. The fragment 2-thrombin complex is only the second cassette module-catalytic domain structure to be determined for a multidomain blood protein and only the third domain-domain interaction to be described among such proteins, the others being factor Xa without a Gla domain and Ca2+ prothrombin fragment 1 with a Gla domain and a kringle. © 1993 American Chemical Society.

Pejibaye palm (Bactris gasipaes) propagative structures and seedlings morphological study

Palm of Arecoideae subfamily, the pejibaye palm occurs mostly at Tropical America areas, and has achieved outstanding economic importance for heart-of-palm production with traditional farming. This work aimed to describe and record propagation structures and seedlings, throughout the different stages of their germination process, since this species is mainly propagated by seeds. The seeds were set for germination on trays with cotton and sterilized water. Representative samples were taken out from each of the different germination stages. They were photographed and drafted using a clear chamber. The propagation structures and seeds external surface were outlined and photographed. The seeds were longitudinally cut for observation and documentation of the inner morphology. The first germinative event was the growth of an undifferentiated, approximately globular cells mass, which emerged from the micropilar depression. Then, the cells mass acquired a cylinder aspect, with the early shoot and root differentiation taking place. Later, there was evidence of primary root and aerial portion. This shoot was coated by a closed and chlorophylled sheath. A lateral root outgrown at the primary root's base and an adventitious root became visible at the embryonic axis. Three other sheaths evolved at the shoot, unrolling one at a time, allowing, finally, the emergence of the primary leaf which is bifid and has parallel veins, typical of its family. Internally, an haustorial structure was developed and seemed to be related with the digestion of the endosperm, occupying, gradually, all the seed's internal space.

RBPI21 interacts with negative membranes endothermically promoting the formation of rigid multilamellar structures

rBPI21 belongs to the antimicrobial peptide and protein (AMP) family. It has high affinity for lipopolysaccharide (LPS), acting mainly against Gram-negative bacteria. This work intends to elucidate the mechanism of action of rBPI21 at the membrane level. Using isothermal titration calorimetry, we observed that rBPI21 interaction occurs only with negatively charged membranes (mimicking bacterial membranes) and is entropically driven. Differential scanning calorimetry shows that membrane interaction with rBPI21 is followed by an increase of rigidity on negatively charged membrane, which is corroborated by small angle X-ray scattering (SAXS). Additionally, SAXS data reveal that rBPI21 promotes the multilamellarization of negatively charged membranes. The results support the proposed model for rBPI21 action: first it may interact with LPS at the bacterial surface. This entropic interaction could cause the release of ions that maintain the packed structure of LPS, ensuring peptide penetration. Then, rBPI21 may interact with the negatively charged leaflets of the outer and inner membranes, promoting the interaction between the two bacterial membranes, ultimately leading to cell death. © 2013 Elsevier B.V.

Subnanometer-resolution structures of the grass carp reovirus core and virion.

Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We report the first subnanometer-resolution three-dimensional structures of both GCRV core and virion by cryoelectron microscopy. These structures have allowed the delineation of interactions among the over 1000 molecules in this enormous macromolecular machine and a detailed comparison with other dsRNA viruses at the secondary-structure level. The GCRV core structure shows that the inner proteins have strong structural similarities with those of orthoreoviruses even at the level of secondary-structure elements, indicating that the structures involved in viral dsRNA interaction and transcription are highly conserved. In contrast, the level of similarity in structures decreases in the proteins situated in the outer layers of the virion. The proteins involved in host recognition and attachment exhibit the least similarities to other members of Reoviridae. Furthermore, in GCRV, the RNA-translocating turrets are in an open state and lack a counterpart for the sigma1 protein situated on top of the close turrets observed in mammalian orthoreovirus. Interestingly, the distribution and the organization of GCRV core proteins resemble those of the cytoplasmic polyhedrosis virus, a cypovirus and the structurally simplest member of the Reoviridae family. Our results suggest that GCRV occupies a unique structure niche between the simpler cypoviruses and the considerably more complex mammalian orthoreovirus, thus providing an important model for understanding the structural and functional conservation and diversity of this enormous family of dsRNA viruses.

Cryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a recently discovered DNA tumor virus that belongs to the gamma-herpesvirus subfamily. Though numerous studies on KSHV and other herpesviruses, in general, have revealed much about their multilayered organization and capsid structure, the herpesvirus capsid assembly and maturation pathway remains poorly understood. Structural variability or irregularity of the capsid internal scaffolding core and the lack of adequate tools to study such structures have presented major hurdles to earlier investigations employing more traditional cryo-electron microscopy (cryoEM) single particle reconstruction. In this study, we used cryo-electron tomography (cryoET) to obtain 3D reconstructions of individual KSHV capsids, allowing direct visualization of the capsid internal structures and systematic comparison of the scaffolding cores for the first time. We show that B-capsids are not a structurally homogenous group; rather, they represent an ensemble of "B-capsid-like" particles whose inner scaffolding is highly variable, possibly representing different intermediates existing during the KSHV capsid assembly and maturation. This information, taken together with previous observations, has allowed us to propose a detailed pathway of herpesvirus capsid assembly and maturation.

Unique structures in a tumor herpesvirus revealed by cryo-electron tomography and microscopy.

Gammaherpesviruses, including the human pathogens Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, are causative agents of lymphomas and other malignancies. The structural characterization of these viruses has been limited due to difficulties in obtaining adequate amount of virion particles. Here we report the first three-dimensional structural characterization of a whole gammaherpesvirus virion by an emerging integrated approach of cryo-electron tomography combined with single-particle cryo-electron microscopy, using murine gammaherpesvirus-68 (MHV-68) as a model system. We found that the MHV-68 virion consists of distinctive envelope and tegument compartments, and a highly conserved nucleocapsid. Two layers of tegument are identified: an inner tegument layer tethered to the underlying capsid and an outer, flexible tegument layer conforming to the overlying, pleomorphic envelope, consistent with the sequential viral tegumentation process inside host cells. Surprisingly, comparison of the MHV-68 virion and capsid reconstructions shows that the interactions between the capsid and inner tegument proteins are completely different from those observed in alpha and betaherpesviruses. These observations support the notion that the inner layer tegument across different subfamilies of herpesviruses has evolved significantly to confer specific characteristics related to viral-host interactions, in contrast to a highly conserved capsid for genome encapsidation and protection.

Benthic foraminiferal composition at the inner wall of the Middle America Trench, Costa Rica

The sediments of Deep Sea Drilling Project Site 565 and University of Texas Marine Science Institute Cores IG-24-7-38 to -42 taken on the landward slope of the Middle America Trench exhibit characteristics of material subject to reworking during downslope mass flow. These characteristics include a generally homogeneous texture, lack of sedimentary structures, pervasive presence of a penetrative scaly fabric, and presence of transported benthic foraminifers. Although these features occur throughout the sediments examined, trends in bulk density, porosity, and water content, and abrupt shifts in these index physical properties and in sediment magnetic properties at Site 565 indicate that downslope sediment creep is presently most active in the upper 45 to 50 m of sediment. It cannot be determined whether progressive dewatering of sediment has brought the material at this depth to a plastic limit at which sediment can no longer flow (thus resulting in its accretion to the underlying sediments) or whether this depth represents a surface along which slumping has occurred. We suspect both are true in part, that is, that mass movements and downslope reworking accumulate sediments in a mobile layer of material that is self-limiting in thickness.