bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial metabolic exchange in 3D
Authors: Watrous Jeramie D , Phelan Vanessa V , Hsu Cheng-Chih , Moree Wilna J , Duggan Brendan M , Alexandrov Theodore , Dorrestein Pieter C
Published: January 2013

Mono- and multispecies microbial populations alter the chemistry of their surrounding environments during colony development thereby influencing multicellular behavior and interspecies interactions of neighboring microbes. Here we present a methodology that enables the creation of three-dimensional (3D) models of a microbial chemotype that can be correlated to the colony phenotype through multimodal imaging analysis. These models are generated by performing matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) imaging mass spectrometry (IMS) on serial cross-sections of microbial colonies grown on 8 mm deep agar, registering data sets of each serial section in MATLAB to create a model, and then superimposing the model with a photograph of the colonies themselves. As proof-of-principle, 3D models were used to visualize metabolic exchange during microbial interactions between Bacillus subtilis and Streptomyces coelicolor, as well as, Candida albicans and Pseudomonas aeruginosa. The resulting models were able to capture the depth profile of secreted metabolites within the agar medium and revealed properties of certain mass signals that were previously not observable using two-dimensional MALDI-TOF IMS. Most significantly, the 3D models were capable of mapping previously unobserved chemical distributions within the array of sub-surface hyphae of C. albicans and how this chemistry is altered by the presence of P. aeruginosa, an opportunistic pathogen known to alter virulence of C. albicans. It was determined that the presence of C. albicans triggered increased rhamnolipid production by P. aeruginosa, which in turn was capable of inhibiting embedded hyphal growth produced beneath the C. albicans colony at ambient temperature.
Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress
Authors: Fan Lu , Liu Michael , Simister Rachel , Webster Nicole S , Thomas Torsten
Published: January 2013

Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associations with complex microbial communities, yet we have a very limited understanding of the detailed biology and ecology of both the host and the symbiont community in response to environmental stressors, such as elevated seawater temperatures. Here, we use the ecologically important sponge Rhopaloeides odorabile as a model to explore the changes in symbiosis during the development of temperature-induced necrosis. Expression profiling of the sponge host was examined in conjunction with the phylogenetic and functional structure and the expression profile of the symbiont community. Elevated temperature causes an immediate stress response in both the host and symbiont community, including reduced expression of functions that mediate their partnership. Disruption to nutritional interdependence and molecular interactions during early heat stress further destabilizes the holobiont, ultimately leading to the loss of archetypal sponge symbionts and the introduction of new microorganisms that have functional and expression profiles consistent with a scavenging lifestyle, a lack virulence functions and a high growth rate. Previous models have postulated various mechanisms of mortality and disease in marine invertebrates. Our study suggests that interruption of symbiotic interactions is a major determinant for mortality in marine sessile invertebrates. High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change.
Proteomic analysis of Mesembryanthemum crystallinum leaf microsomal fractions finds an imbalance in V-ATPase stoichiometry during the salt-induced transition from C3 to CAM
Authors: Cosentino Cristian , Di Silvestre Dario , Fischer-Schliebs Elke , Homann Ulrike , De Palma Antonella , Comunian Claudio , Mauri Pier Luigi , Thiel Gerhard
Published: January 2013

The halophyte Mesembryanthemum crystallinum adapts to salt stress by salt uptake and switching from C3 photosynthesis to CAM (crassulacean acid metabolism). An important role in this process is played by transport proteins in the tonoplast of the central vacuole. In the present study we examine dynamic changes in the protein composition during salt-stress adaptation in microsomes from M. crystallinum leaves. Plants challenged with 400 mM NaCl accumulate salt by day 4 of treatment and malic acid only at day 12; a switching to CAM hence follows any initial steps of salt adaptation with a delay. Using a label-free and semiquantitative approach, we identified the most dramatic changes between the proteome of control plants and plants harvested after 12 days of the treatment; the abundance of 14 proteins was significantly affected. The proteomic data revealed that the majority of the subunits of V-ATPase (vacuolar H+-ATPase) holoenzyme. The salt treatment somewhat decreased the abundance of all subunits in the short term (4 days). Long-term adaptation, including the switching to CAM, goes together with a strong increase in the representation of all detectable subunits. Because this increase is subunit-specific, with the highest rise occurring for subunits E and c, the data suggest that long-term adaptation to salt stress correlates with a change in V-ATPase subunit stoichiometry and highlight the structural plasticity of this holoenzyme.
Structure and mechanism of the PilF DNA transformation ATPase from Thermus thermophilus
Authors: Collins Richard F. , Hassan Darin , Karuppiah Vijaykumar , Thistlethwaite Angela , Derrick Jeremy P.
Published: January 2013

Many Gram-negative bacteria contain specific systems for uptake of foreign DNA, which play a critical role in the acquisition of antibiotic resistance. The TtPilF (PilF ATPase from Thermus thermophilus) is required for high transformation efficiency, but its mechanism of action is unknown. In the present study, we show that TtPilF is able to bind to both DNA and RNA. The structure of TtPilF was determined by cryoelectron microscopy in the presence and absence of the ATP analogue p[NH]ppA (adenosine 5′-[β,γ-imido]triphosphate), at 10 and 12 Å (1 Å=0.1 nm) resolutions respectively. It consists of two distinct N- and C-terminal regions, separated by a short stem-like structure. Binding of p[NH]ppA induces structural changes in the C-terminal domains, which are transmitted via the stem to the N-terminal domains. Molecular models were generated for the apoenzyme and p[NH]ppA-bound states in the C-terminal regions by docking of a model based on a crystal structure from a closely related enzyme. Analysis of DNA binding by electron microscopy, using gold labelling, localized the binding site to the N-terminal domains. The results suggest a model in which DNA uptake by TtPilF is powered by ATP hydrolysis, causing conformational changes in the C-terminal domains, which are transmitted via the stem to take up DNA into the cell.
Subtype-selective regulation of IP3 receptors by thimerosal via cysteine residues within the IP3-binding core and suppressor domain
Authors: Khan Samir A. , Rossi Ana M. , Riley Andrew M. , Potter Barry V. L. , Taylor Colin W.
Published: January 2013

IP3R (IP3 [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca2+ channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP3R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP3-evoked Ca2+ release via IP3R1 and IP3R2, but inhibited IP3R3. Activation of IP3R is initiated by IP3 binding to the IBC (IP3-binding core; residues 224–604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1–223). Thimerosal (100 μM) stimulated IP3 binding to the isolated NT (N-terminal; residues 1–604) of IP3R1 and IP3R2, but not to that of IP3R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP3) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP3R activation. IP3 binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP3R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP3 binding to the chimaeric NT and IP3-evoked Ca2+ release from the chimaeric IP3R. This is the first systematic analysis of the effects of a thiol reagent on each IP3R subtype. We conclude that thimerosal selectively sensitizes IP3R1 and IP3R2 to IP3 by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor.
Regulation of ubiquitin transfer by XIAP, a dimeric RING E3 ligase
Authors: Nakatani Yoshio , Kleffmann Torsten , Linke Katrin , Condon Stephen M. , Hinds Mark G. , Day Catherine L.
Published: January 2013

RING domains of E3 ligases promote transfer of Ub (ubiquitin) from the E2~Ub conjugate to target proteins. In many cases interaction of the E2~Ub conjugate with the RING domain requires its prior dimerization. Using cross-linking experiments we show that E2 conjugated ubiquitin contacts the RING homodimer interface of the IAP (inhibitor of apoptosis) proteins, XIAP (X-linked IAP) and cIAP (cellular IAP) 2. Structural and biochemical analysis of the XIAP RING dimer shows that an aromatic residue at the dimer interface is required for E2~Ub binding and Ub transfer. Mutation of the aromatic residue abolishes Ub transfer, but not interaction with Ub. This indicates that nuleophilic attack on the thioester bond depends on precise contacts between Ub and the RING domain. RING dimerization is a critical activating step for the cIAP proteins; however, our analysis shows that the RING domain of XIAP forms a stable dimer and its E3 ligase activity does not require an activation step.
Small particles, big impacts: A review of the diverse applications of nanofluids
Authors: Taylor Robert , Coulombe Sylvain , Otanicar Todd , Phelan Patrick , Gunawan Andrey , Lv Wei , Rosengarten Gary , Prasher Ravi , Tyagi Himanshu
Published: January 2013

Nanofluids—a simple product of the emerging world of nanotechnology—are suspensions of nanoparticles (nominally 1–100 nm in size) in conventional base fluids such as water, oils, or glycols. Nanofluids have seen enormous growth in popularity since they were proposed by Choi in 1995. In the year 2011 alone, there were nearly 700 research articles where the term nanofluid was used in the title, showing rapid growth from 2006 (175) and 2001 (10). The first decade of nanofluid research was primarily focused on measuring and modeling fundamental thermophysical properties of nanofluids (thermal conductivity, density, viscosity, heat transfer coefficient). Recent research, however, explores the performance of nanofluids in a wide variety of other applications. Analyzing the available body of research to date, this article presents recent trends and future possibilities for nanofluids research and suggests which applications will see the most significant improvement from employing nanofluids.
Dynamic criticality at the jamming transition
Authors: Ikeda Atsushi , Berthier Ludovic , Biroli Giulio
Published: January 2013

We characterize vibrational motion occurring at low temperatures in dense suspensions of soft repulsive spheres over a broad range of volume fractions encompassing the jamming transition at (T = 0, φ = φJ). We find that characteristic time and length scales of thermal vibrations obey critical scaling in the vicinity of the jamming transition. We show in particular that the amplitude and the time scale of dynamic fluctuations diverge symmetrically on both sides of the transition, and directly reveal a diverging correlation length. The critical region near φJ is divided in three different regimes separated by a characteristic temperature scale T⋆(φ) that vanishes quadratically with the distance to φJ. While two of them, (T < T⋆(φ), φ > φJ) and (T < T⋆(φ), φ < φJ), are described by harmonic theories developed in the zero temperature limit, the third one for T > T⋆(φ) is inherently anharmonic and displays new critical properties. We find that the quadratic scaling of T⋆(φ) is due to nonperturbative anharmonic contributions, its amplitude being orders of magnitude smaller than the perturbative prediction based on the expansion to quartic order in the interactions. Our results show that thermal vibrations in colloidal assemblies directly reveal the critical nature of the jamming transition. The critical region, however, is very narrow and has not yet been attained experimentally, even in recent specifically-dedicated experiments.
Are polar liquids less simple?
Authors: Fragiadakis D. , Roland C. M.
Published: January 2013

Strong correlation between equilibrium fluctuations under isochoric conditions of the potential energy, U, and the virial, W, is a characteristic of liquids that implies the presence of certain dynamic properties, such as density scaling of the relaxation times and isochronal superpositioning of the relaxation function. In this work we employ molecular dynamics simulations on methanol and two variations, lacking hydrogen bonds and a dipole moment, to assess the connection between the correlation of U and W and these dynamic properties. We show, in accord with prior results of others [T. S. Ingebrigtsen, T. B. Schrøder, and J. C. Dyre, Phys. Rev. X 2, 011011 (2012)10.1103/PhysRevX.2.011011], that simple van der Waals liquids exhibit both strong correlations and the expected dynamic behavior. However, for polar liquids this correspondence breaks down—weaker correlation between U and W is not associated with worse conformance to density scaling or isochronal superpositioning. The reason for this is that strong correlation between U and W only requires their proportionality, whereas the expected dynamic behavior depends primarily on constancy of the proportionality constant for all state points. For hydrogen-bonded liquids, neither strong correlation nor adherence to the dynamic properties is observed; however, this nonconformance is not directly related to the concentration of hydrogen bonds, but rather to the greater deviation of the intermolecular potential from an inverse power law (IPL). Only (hypothetical) liquids having interactions governed strictly by an IPL are perfectly correlating and exhibit the consequent dynamic properties over all thermodynamic conditions.
Assessment of the role of axial vorticity in the formation of particle accumulation structures in supercritical Marangoni and hybrid thermocapillary-rotation-driven flows
Authors: Lappa Marcello
Published: January 2013

Evidence is provided that when the so-called phenomenon of particle accumulation structure (PAS) occurs, extended regions exist where ½ of the axial component of vorticity matches the angular frequency of the traveling wave produced by the instability of the Marangoni flow. Several cases are considered in which such axial component is varied by “injecting” vorticity into the system via rotation of one of its endwalls. The results show that both the resulting PAS lines and the trajectories of related solid particles undergo significant changes under the influence of imposed rotation. By analysis of such findings, a validation and a generalization/extension of the so-called “phase-locking” model are provided.
Directional-dependent coercivities and magnetization reversal mechanisms in fourfold ferromagnetic systems of varying sizes
Authors: Blachowicz T. , Ehrmann A. , Stebliński P. , Palka J.
Published: January 2013

Different types of reversal processes, including either uniform-rotation or domain-wall driven processes, were indentified in magnetic nano-wires of four-fold symmetry using micromagnetic simulations. Iron wires were tested for diameters ranging from 6 nm up to 20 nm, while their lengths were taken from 30 nm to 70 nm range, and for several directions of externally applied magnetic field. Physical parameters of presented low-dimensional structures enabled reversal via intermediate states, which can lead to additional stable states at remanence, contrary to instable vortexes observed in magnetic nano-rings or cylindrical nanodots.
Equations of motion solved by the Cremmer-Scherk configuration on even-dimensional spheres
Authors: Kihara Hironobu
Published: January 2013

Equations of motion of low-energy effective theories of quantum electrodynamics include infinitely many interaction terms, which make them difficult to solve. The self-duality property has facilitated research on the solutions to these equations. In this paper, equations of motion of systems of non-Abelian gauge fields on even-dimensional spheres are considered. It is demonstrated that the Cremmer-Scherk configuration, which satisfies certain generalized self-duality equations, becomes the classical solution for the class of systems that are given by arbitrary functions of class C1 of 2m + 1 quantities. For instance, Lagrangians consisting of multi-trace terms are included in this class. This result is likely to generate several new and interesting directions of research, including the classification of actions with respect to the stability condition against the Cremmer-Scherk configuration.
Improved reliability predictions in high permittivity dielectric oxide capacitors under high dc electric fields with oxygen vacancy induced electromigration
Authors: Randall C. A. , Maier R. , Qu W. , Kobayashi K. , Morita K. , Mizuno Y. , Inoue N. , Oguni T.
Published: January 2013

This paper attempts to improve upon the range of applicability and predictability of the empirical highly accelerated lifetime testing (HALT) equation that has been traditionally used to estimate time dependent breakdown strength performance in multilayer ceramic capacitors (MLCC) and integrated thin film capacitor structures. The present and traditional HALT equation shows evidence of being limited in thin dielectric layers under high fields, for example, in high capacitance MLCCs. When the traditional HALT equations are applied to MLCCs with higher operating electric fields, there are often field dependent voltage acceleration factors resulting in ambiguous data analysis. Here, we introduce a physical model to account for a critical ionic space charge accumulation preceded by the ionic hopping or electromigration of oxygen vacancies leading to an ultimate increase in leakage current typical of dielectric resistance degradation. Mean time to failure degradation data on experimental capacitors indicates superior predictions with the new non-linear equation than with the traditional HALT equation to provide more accurate and simpler testing in future components. It is further noted that this approach may be applicable to many capacitive devices that operate under a high bias and can have ionic space charge accumulation at interfaces prior to breakdown.
Infrared to vacuum-ultraviolet ellipsometry and optical Hall-effect study of free-charge carrier parameters in Mg-doped InN
Authors: Schöche S. , Hofmann T. , Darakchieva V. , Ben Sedrine N. , Wang X. , Yoshikawa A. , Schubert M.
Published: January 2013

Infrared to vacuum-ultraviolet spectroscopic ellipsometry and far-infrared optical Hall-effect measurements are applied to conclude on successful p-type doping of InN films. A representative set of In-polar Mg-doped InN films with Mg concentrations ranging from 1.2×1016 cm−3 to 3.9×1021 cm−3 is investigated. The data are compared and discussed in dependence of the Mg concentration. Differences between n-type and p-type conducting samples are identified and explained. p-type conductivity in the Mg concentration range between 1.1×1018 cm−3 and 2.9×1019 cm−3 is indicated by the appearance of a dip structure in the infrared spectral region related to a loss in reflectivity of p-polarized light as a consequence of reduced LO phonon plasmon coupling, by vanishing free-charge carrier induced birefringence in the optical Hall-effect measurements, and by a sudden change in phonon-plasmon broadening behavior despite continuous change in the Mg concentration. By modeling the near-infrared-to-vacuum-ultraviolet ellipsometry data, information about layer thickness, electronic interband transitions, as well as surface roughness is extracted in dependence of the Mg concentration. A parameterized model that accounts for the phonon-plasmon coupling is applied for the infrared spectral range to determine the free-charge carrier concentration and mobility parameters in the doped bulk InN layer as well as the GaN template and undoped InN buffer layer. The optical Hall-effect best-match model parameters are consistent with those obtained from infrared ellipsometry analysis.
Reactive sputter magnetron reactor for preparation of thin films and simultaneous in situ structural study by X-ray diffraction
Authors: Bürgi J. , Neuenschwander R. , Kellermann G. , Molleja J. García , Craievich A. F. , Feugeas J.
Published: January 2013

The purpose of the designed reactor is (i) to obtain polycrystalline and/or amorphous thin films by controlled deposition induced by a reactive sputtering magnetron and (ii) to perform a parallel in situ structural study of the deposited thin films by X-ray diffraction, in real time, during the whole growth process. The designed reactor allows for the control and precise variation of the relevant processing parameters, namely, magnetron target-to-sample distance, dc magnetron voltage, and nature of the gas mixture, gas pressure and temperature of the substrate. On the other hand, the chamber can be used in different X-ray diffraction scanning modes, namely, θ-2θ scanning, fixed α-2θ scanning, and also low angle techniques such as grazing incidence small angle X-ray scattering and X-ray reflectivity. The chamber was mounted on a standard four-circle diffractometer located in a synchrotron beam line and first used for a preliminary X-ray diffraction analysis of AlN thin films during their growth on the surface of a (100) silicon wafer.
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity
Authors: Frigori Rafael B. , Rizzi Leandro G. , Alves Nelson A.
Published: January 2013

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.
Comment on “The limits of flexoelectricity in liquid crystals” [AIP Advances 1, 032120 (2011)]
Authors: Palffy-Muhoray P.
Published: January 2013

In their paper, using the principle of energy conservation, F. Castles, S. M. Morris, and H. J. Coles [AIP Advances 1, 032120 (2011)]10.1063/1.3624725 establish inequalities involving the elastic and dielectric constants and flexoelectric coefficients of liquid crystals. They then argue that recently measured values of flexoelectric coefficients by Harden et al. do not obey these inequalities, hence they violate the principle of energy conservation. In this comment, we point out that in their calculation, Castles et al. use an inappropriate value for an elastic constant, hence their conclusions, predicated on the outcome of this calculation, are not justified.
Polymer-polymer adhesion with mobile promoters: Connector areal density dependence
Authors: Zhang Bin
Published: January 2013

The adhesion between two immiscible polymers stitched together via mobile promoters is studied with large scale molecular simulations employing a coarse-grained bead-spring model. An adhesion model is presented that enables both connector molecular slipping out viscously and bulk dissipation in two dissimilar glassy polymers, in which one is dense melt and another is loose. The contributions to the separation work from thermodynamics and chain suction are studied in dependence of the connector areal density, at constant temperature, and at fixed basic molecular parameters. It is shown that high connector coverage, but below saturation areal density, can enhance the adhesion toughness and interfacial strength. Bulk dissipation is not considerable with low connector areal density in mushroom regime, while becomes more evident in the loose block when the coverage density is increased up to overlapping brush regime. With increasing connector length, both bulk melts are enhanced by the segments of connector chains that penetrated in. The results provide insight into the structure evolution of adhesion interface coupled with promoter molecular, which are useful for future developments of continuum cohesive models for fracture of polymer- polymer interfaces.
Mixed phase Ge2Sb2Te5 thin films with temperature independent resistivity
Authors: Privitera S. , Garozzo C. , Alberti A. , Perniola L. , De Salvo B.
Published: January 2013

The electrical properties of polycrystalline Ge2Sb2Te5 thin films containing both the metastable fcc phase and the stable hcp phase have been studied. The resistivity and its temperature dependence have been modelled using effective medium approximation. By varying the volume fraction of the two phases it is possible to get films with different resistivities and temperature coefficient of resistance, changing without discontinuity from negative (fcc) to positive value (hcp). Mixed phase films with resistivity almost independent of the temperature are obtained at about 4 mΩ cm.
The Role of Movement Synchronization with an Auditory Signal in Producing Prism Adaptation
Authors: Bornschlegl Mona A , Fahle Manfred , Redding Gordon M
Published: January 2013

The prism adaptation procedure is often used to study the plasticity of eye-hand coordination to misalignment of the visual and proprioceptive spatial maps. Misalignment can be resolved by adaptive change in spatial maps of either the eyes or hand or both. In this procedure, pacing pointing movements with a rhythmic auditory signal is usually employed to control movement speed, but the role of the auditory signal itself in producing adaptation has not been examined. The present experiment addressed this issue by testing three conditions: (i) exposure pointing was self-paced without an auditory signal; (ii) exposure pointing was paced by an auditory signal without synchronization; and (iii) exposure pointing was synchronized with the auditory signal. The first condition produced primarily proprioceptive adaptation. The second condition also produced primarily proprioceptive adaptation, but visual adaptation was also present. The third condition produced primarily visual adaptation. Results are discussed in terms of two possible roles for the auditory signal: (i) a rhythmic auditory signal may enhance overall activation of the adaptive neural network; and (ii) movement synchronization with a rhythmic auditory signal may enable multisensory integration, including auditory spatial information that selects the more reliable proprioceptive signal for movement control. Consequently, detection of the misalignment is localized and realignment occurs in the visual system.
The Vision of David Marr
Authors: Stevens Kent A
Published: January 2013

Marr proposed a computational paradigm for studying the visual system, wherein aspects of vision would be amenable to study with what might be regarded a computational-reductionist approach. First, vision would be cleaved into separable ‘computational theories’, in which the visual system is characterized in terms of its computational goals and the strategies by which they are carried out. Each such computational theory could then be investigated in increasingly concrete terms, from symbols and measurements, to representations and algorithms, to processes and neural implementations. This paradigm rests on some general expectations of a symbolic information processing system, including his stated principles of explicit naming, modular design, least commitment, and graceful degradation. In retrospect, the computational framework also tacitly rests on additional assumptions about the nature of biological information processing: (1) separability of computational strategies, (2) separability of representations, (3) a pipeline nature of information processing, and that (4) the representations employ primitives of low dimensionality. These assumptions are discussed in this retrospective.
On the axiomatization of convex subsets of Banach spaces
Authors: Capraro Valerio , Fritz Tobias
Published: January 2013

We prove that any convex-like structure in the sense of Nate Brown is affinely and isometrically isomorphic to a closed convex subset of a Banach space. This answers an open question of Brown. As an intermediate step, we identify Brown’s algebraic axioms as equivalent to certain well-known axioms of abstract convexity. We conclude with a new characterization of convex subsets of Banach spaces.
Binomial arithmetical rank of edge ideals of forests
Authors: Kimura Kyouko , Terai Naoki
Published: January 2013

We prove that the binomial arithmetical rank of the edge ideal of a forest coincides with its big height.
Microbiota and Gut–Liver Axis
Authors: Vajro Pietro , Paolella Giulia , Fasano Alessio
Published: January 2013

A specific bacterial gut microbiota profile with increased extraction of energy has recently been associated with obesity, which has been shown to be a transmissible phenotype by microbiota transplantation. At the same time, there is now increasing evidence that gut microbiota plays a role in the development of hepatic steatosis and its progression to nonalcoholic steatohepatitis. This review summarizes well known and unexpected interacting factors leading to obesity and its related hepatic diseases, including intestinal mucosal permeability and its regulation, gut microbiota and translocation of its biological products, and gut‐associated lymphoid tissue. These intestinal factors dictate also the balance between tolerance and immune response, which are critical for most of the complications in near and far organs or systems. We review novel mechanisms involving the development of gut permeability and adipose tissue plasticity, for example, the cross‐talk between the gut microbiota, lipopolysaccharide, high‐fat diet, and the endocannabinoid system tone, which have not been fully explored. Interactions between gut microbiota and other factors (eg, inflammasome deficiency) also are reviewed as emerging but far from being completely elucidated mechanisms influencing the onset of obesity and nonalcoholic fatty liver disease.
Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways
Authors: Qi Yiping , Zhang Yong , Zhang Feng , Baller Joshua A. , Cleland Spencer C. , Ryu Yungil , Starker Colby G. , Voytas Daniel F.
Published: January 2013

Improved methods for engineering sequence-specific nucleases, including zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs), have made it possible to precisely modify plant genomes. However, the success of genome modification is largely dependent on the intrinsic activity of the engineered nucleases. In this study, we sought to enhance ZFN-mediated targeted mutagenesis and gene targeting (GT) in Arabidopsis by manipulating DNA repair pathways. Using a ZFN that creates a double-strand break (DSB) at the endogenous ADH1 locus, we analyzed repair outcomes in the absence of DNA repair proteins such as KU70 and LIG4 (both involved in classic nonhomologous end-joining, NHEJ) and SMC6B (involved in sister-chromatid-based homologous recombination, HR). We achieved a fivefold to 16-fold enhancement in HR-based GT in a ku70 mutant and a threefold to fourfold enhancement in GT in the lig4 mutant. Although the NHEJ mutagenesis frequency was not significantly changed in ku70 or lig4, DNA repair was shifted to microhomology-dependent alternative NHEJ. As a result, mutations in both ku70 and lig4 were predominantly large deletions, which facilitates easy screening for mutations by PCR. Interestingly, NHEJ mutagenesis and GT at the ADH1 locus were enhanced by sixfold to eightfold and threefold to fourfold, respectively, in a smc6b mutant. The increase in NHEJ-mediated mutagenesis by loss of SMC6B was further confirmed using ZFNs that target two other Arabidopsis genes, namely, TT4 and MPK8. Considering that components of DNA repair pathways are highly conserved across species, mutations in DNA repair genes likely provide a universal strategy for harnessing repair pathways to achieve desired targeted genome modifications.
9-[3-(Dimethylamino)propyl]-10,10-dimethyl-9,10-dihydroanthracen-9-ol
Authors: Kaur Manpreet , Butcher Ray J. , Akkurt Mehmet , Yathirajan H. S. , Nagaraj B.
Published: January 2013

The asymmetric unit of the title compound, C21H27NO, contains two molecules (AandB). In moleculeA, the central ring of the anthrone unit adopts a shallow boat conformation and the dihedral angle between the benzene rings is 18.96 (7)°. In moleculeB, the central ring is close to being planar (r.m.s. deviation = 0.078 Å) and the dihedral angle between the aromatic rings is 7.82 (7)°. In the crystal, molecules are linked by O—H...N hydrogen bonds, forming zigzagC(7) chains of alternatingAandBmolecules running parallel to [100]. The structure also features weak C—H...O and C—H...π interactions.
2-[5-(2-Fluorophenyl)-3-isobutyl-1H-pyrazol-1-yl]benzoic acid
Authors: Sreenivasa S. , Manojkumar K. E. , Suchetan P. A. , Mohan N. R. , Kumar Vijith , Palakshamurthy B. S.
Published: January 2013

In the title compound, C20H19FN2O2, the dihedral angle between the aromatic rings is 62.1 (1)°, and those between the pyrazole ring and the fluorobenzene and benzoic acid rings are 52.1 (1) and 53.1 (1)°, respectively. In the crystal, molecules are linked into [010]C(7) chains by O—H...N hydrogen bonds.
BenzylN-[(Z)-(1-methyl-2-sulfanylpropylidene)amino]carbamodithioate
Authors: Break Mohammed Khaled bin , Mehta Sachin , Tahir M. Ibrahim M. , Crouse Karen A. , Khoo Teng-Jin
Published: January 2013

The title compound, C12H16N2S3, was obtained by the condensation reaction ofS-benzyl dithiocarbazate and 3-mercaptobutan-2-one. The phenyl ring and thiol (SH) group are approximately perpendicular [S—C—C—C and N—C—C—S torsion angles = 67.8 (3) and 116.9 (2)°, respectively] to the rest of the molecule. In the crystal, molecules are linked by weak S—H...S and N—H...S hydrogen bonds, π–π interactions between the benzene rings [centroid–centroid distance = 3.823 (2) Å] and C—H...π interactions.
N-(7-Dibromomethyl-5-methyl-1,8-naphthyridin-2-yl)acetamide–pyrrolidine-2,5-dione (1/1)
Authors: Gou Gao-Zhang , Kou Jun-Feng , Zhou Qing-Di , Chi Shao-Ming
Published: January 2013

In the title co-crystal, C12H11Br2N3O·C4H5NO2, the naphthyridine derivative and the pyrrolidine-2,5-dione molecules have crystallographic mirror-plane symmetry with all non-H atoms, except the Br atom, located on the mirror plane. In the crystal, N—H...N, N—H...O and C—H...O hydrogen bonds link the molecules into heterodimers. These dimers are further linked into a one-dimensional structure along [010] by weak C—Br...O interactions [Br...O = 3.028 (5) Å and C—Br...O = 158.52 (4)°].
A second monoclinic polymorph ofN-(2,4-dinitrophenyl)-2,4-dinitroaniline
Authors: Tokutome Yui , Okuno Tsunehisa
Published: January 2013

The title compound, C12H7N5O8, was previously described in space groupP21/nwithZ= 4 [Wuet al.(2007).Acta Cryst.E63, o4194]. The current monoclinicP21/cpolymorph was obtained from a mixed solution of dichloromethane and hexane. The dihedral angle between the benzene rings is 44.16 (5)°, smaller than in the previously reported polymorph [56.3 (2)°]. As a result of the steric hinderance of the nitro groups, hydrogen bonding is limited intramolecularly. The dihedral angles between the phenyl rings and their attached nitro groups are 18.97 (6) and 17.71 (5)° at the 2-position, and 18.52 (6) and 32.41 (6)° at the 4-position.
6-Bromo-1-methyl-4-[2-(1-phenylethylidene)hydrazinylidene]-3,4-dihydro-1H-2λ6,1-benzothiazine-2,2-dione
Authors: Shafiq Muhammad , Tahir M. Nawaz , Harrison William T. A. , Bukhari Iftikhar Hussain , Khan Islam Ullah
Published: January 2013

In the title compound, C17H16BrN3O2S, the dihedral angle between the aromatic rings is 1.24 (15)° and the C=N—N=C torsion angle is 167.7 (3)°. The conformation of the thiazine ring is an envelope, with the S atom displaced by 0.805 (3) Å from the mean plane of the other five atoms (r.m.s. deviation = 0.027 Å). In the crystal, C—H...O interactions link the molecules intoC(10) [010] chains. A weak C—H...π interaction is also observed.
1-{(Z)-[2-Methoxy-5-(trifluoromethyl)anilino]methylidene}naphthalen-2(1H)-one
Authors: Kargılı Hakan , Alaman Ağar Ayşen , Alpaslan Gökhan , Büyükgüngör Orhan , Erdönmez Ahmet
Published: January 2013

The title compound, C19H14F3NO2, crystallizes in the keto–amine tautomeric form, with a strong intramolecular N—H...O hydrogen bond. The molecule is almost planar; the dihedral angle between the naphthalene ring system and the benzene ring is 4.60 (7)°. In the crystal, molecules are linked into chains along thecaxis by C—H...O hydrogen bonds. The F atoms of the trifluoromethyl group are disordered over two positions with refined site occupancies of 0.668 (9) and 0.332 (9).
3-({4-[(2-Methylbenzylidene)amino]-5-sulfanylidene-1H-1,2,4-triazol-3-yl}methyl)-1,3-benzoxazol-2(3H)-one
Authors: Aydın Abdullah , Hekimoğlu Nuray , Akkurt Mehmet , Önkol Tijen , Çiçekli Şölen Urlu , Büyükgüngör Orhan
Published: January 2013

In the title compound, C18H15N5O2S, a weak intramolecular C—H...S hydrogen bond results in a small dihedral angle of 3.71 (9)° between the methylphenyl and triazole rings, which, in turn, form dihedral angles of 80.09 (8) and 77.32 (8)°, respectively, with the benzoxazolone mean plane. In the crystal, N—H...O hydrogen bonds link molecules into chains along [001], and weak C—H...N hydrogen bonds and π–π interactions between the five- and six-membered rings [centroid–centroid distances = 3.5074 (11) and 3.616 (1) Å] consolidate the crystal packing.
(1SR,3RS,3aSR,6aRS)-Methyl 5-methyl-4,6-dioxo-3-[2-(trifluoromethyl)phenyl]octahydropyrrolo[3,4-c]pyrrole-1-carboxylate
Authors: Kudryavtsev Konstantin V. , Ivantcova Polina M. , Churakov Andrei V.
Published: January 2013

In the title compound, C16H15F3N2O4, the relative stereochemistry of the four stereogenic C atoms has been determined. The carboxymethyl and 2-(trifluoromethyl)phenyl substituents of the pyrrolidine cycle have acismutual arrangement. The five-membered saturated azacycle adopts an envelope conformation with the N atom occupying the flap position. In the crystal, adjacent molecules are combined in centrosymmetric dimers by two weak N—H...O hydrogen bonds.
4-[Amino(3-methylphenyl)methylidene]-2-(3-methylphenyl)-1H-imidazol-5(4H)-one ethanol hemisolvate
Authors: Prabhuswamy M. , Madan Kumar S. , Muneer C. P. , Shafi P. M. , Lokanath N. K.
Published: January 2013

In the title compound, C18H17N3O·0.5C2H5OH, the dihedral angles between the central imidazole rings and the pendant benzene rings are 42.06 (15) and 2.01 (16)° in one asymmetric molecule and 47.91 (15) and 7.31 (14)° in the other. An intramolecular N—H...O hydrogen bond occurs in each imidazole molecule. In the crystal, the components are connected by O—H...N, N—H...O, C—H...O and N—H...N hydrogen bonds. Weak aromatic π–π interactions also occur [shortest centroid–centroid distance = 3.684 (3) Å].
1-(4-Chlorophenyl)-2-[tris(4-methylphenyl)-λ5-phosphanylidene]butane-1,3-dione
Authors: Sabounchei Seyyed Javad , Shahriary Parisa , Hosseini Fashami Faegheh , Morales-Morales David , Hernandez-Ortega Simon
Published: January 2013

In the title ylide, C31H28ClO2P [common name α-acetyl-α-p-chlorobenzoylmethylenetri(p-tolyl)phosphorane], the dihedral angle between the 4-chlorophenyl ring and that of the ylide moiety is 66.15 (10)°. The geometry around the P atom is slightly distorted tetrahedral [angle range = 105.22 (8)–115.52 (9)°] and the carbonyl O atoms aresyn-oriented with respect to the P atom. The ylide group is close to planar [maximum deviation from the least-squares plane = 0.006 (2) Å] and the P—C, C—C and C=O bond lengths are consistent with electron delocalization involving the O atoms.
(2,3-Difluorophenyl)(4-tosylpiperazin-1-yl)methanone
Authors: Sreenivasa S. , ManojKumar K. E. , Suchetan P. A. , Tonannavar J. , Chavan Yashshwita , Palakshamurthy B. S.
Published: January 2013

In the title compound, C18H18F2N2O3S, the piperazine ring adopts a chair conformation. The dihedral angle between the sulfonyl-bound benzene ring and the best fit plane throught the six non-H atoms of the piperazine ring is 69.4 (2)°, while those between the fluorobenzene and sulfonyl rings and the fluorobenzene and piperazine rings are 30.97 (2) and 75.98 (2)°, respectively. In the crystal, molecules are connected to form a tetrameric unit through C—H...O hydrogen bonds. The structure is further stabilized by weak intermolecular C—H...F interactions, generatingC(8) andC(7) chains running along [100].
Methyl 6-ethoxy-3-phenyl-3a,4-dihydro-3H-chromeno[4,3-c]isoxazole-3a-carboxylate
Authors: Suresh G. , Srinivasan J. , Bakthadoss M. , Aravindhan S.
Published: January 2013

In the title compound, C20H19NO5, the dihedral angle between the mean plane of the pyran ring (which has a half-chair conformation) and the benzene ring of the chromeno ring system is 7.21 (7)°. The dihedral angle between the mean plane of the chromeno ring system and the isoxazole ring is 21.78 (6)°, while the isoxazole ring forms a dihedral angle of 72.60 (8)° with the attached phenyl ring. In the crystal, molecules are linkedviapairs of C—H...O hydrogen bonds, forming inversion dimers with anR22(10) ring motif. These dimers are linkedviaC—H...N hydrogen bonds, forming chains along [001].
3-(2-Methylphenyl)-3a,4-dihydro-3H-chromeno[4,3-c]isoxazole-3a-carbonitrile
Authors: Suresh G. , Srinivasan J. , Bakthadoss M. , Aravindhan S.
Published: January 2013

In the title compound, C18H14N2O2, the pyran ring of the chromeno ring system has a half-chair conformation, and the dihedral angle between its mean plane and the benzene ring is 5.3 (2)°. The isoxazole ring forms a dihedral angle of 74.6 (2)° with the attached benzene ring and is inclined to the mean plane of the chromeno ring system by 15.06 (19)°. In the crystal, there are no significant intermolecular interactions.
2-(2H-Indazol-2-yl)-1-phenylethanone
Authors: Özel Güven Özden , Türk Gökhan , Adler Philip D. F. , Coles Simon J. , Hökelek Tuncer
Published: January 2013

The asymmetric unit of the title compound, C15H12N2O, contains two independent molecules with different conformations, the phenyl ring and indazole mean plane in the two molecules forming dihedral angles of 50.82 (5) and 89.29 (6)°. In the crystal, weak C—H...O and C–H...N hydrogen bonds and C—H...π interactions consolidate the packing.
Influence of seawater composition on SCC behavior of anodized 1050 Al‐alloy
Authors: Spathis P. , Papastergiadis E.
Published: January 2013

Purpose

The purpose of this paper is to study the stress corrosion cracking (SCC) behaviour of anodized 1050 Al‐alloy in marine environments at different concentrations of sulphate ions.

Design/methodology/approach

The SCC experiments were performed by measuring the time to failure in 3.5% NaCl solution, or in the presence of three different concentrations of sulphate ions under conditions of applied anodic current. For the interpretation of the results, changes in potential during SCC tests and optical microscope micrographs of stress corrosion tested specimens at various periods of time, were obtained.

Findings

The influence of seawater composition on the SCC behaviour of the anodized 1050 Al‐alloy depends on the concentration of sulphate ions, the oxide thickness and the stress level. At the higher stress levels and low concentrations of sulphate ions, increased times to failure were observed. These results were attributed to the inhibitory action of sulphate ions. At a low stress level and higher concentration of sulphate ions, the increased times of exposure and the more intensive corrosive environment led to partial destruction of the anodic coatings and a decrease in the time to failure. Better protective properties were observed at an oxide thickness of 10 μm. The thicker oxides did not protect so well because they were more brittle, cracking under strain and allowing corrosive species to reach the metal surface.

Research limitations/implications

The hypothesised mechanism of the effect of seawater composition on the SCC behaviour of anodized Al‐alloys depended on the concentration of sulphate ions and the stress level remains yet to be confirmed.

Practical implications

The selection of suitable anodic coatings for the protection of aluminium alloys against stress corrosion cracking depends on the composition of the marine environment.

Originality/value

The paper provides information regarding the influence of sulphate ions on the anticorrosive properties of electrolytically prepared anodic coatings on aluminium alloys.