bluuebunny/crossref_metadata_2025 huggingface dataset:
An interactive, visual approach to developing and applying parametric three-dimensional spatial grammars
Authors: Hoisl Frank , Shea Kristina
Published: October 2011

Spatial grammars are rule based, generative systems for the specification of formal languages. Set and shape grammar formulations of spatial grammars enable the definition of spatial design languages and the creation of alternative designs. Since the introduction of the underlying formalism, they have been successfully applied to different domains including visual arts, architecture, and engineering. Although many spatial grammars exist on paper, only a few, limited spatial grammar systems have been computationally implemented to date; this is especially true for three-dimensional (3-D) systems. Most spatial grammars are hard-coded, that is, once implemented, the vocabulary and rules cannot be changed without reprogramming. This article presents a new approach and prototype implementation for a 3-D spatial grammar interpreter that enables interactive, visual development and application of grammar rules. The method is based on a set grammar that uses a set of parameterized primitives and includes the definition of nonparametric and parametric rules, as well as their automatic application. A method for the automatic matching of the left hand side of a rule in a current working shape, including defining parametric relations, is outlined. A prototype implementation is presented and used to illustrate the approach through three examples: the “kindergarten grammar,” vehicle wheel rims, and cylinder cooling fins. This approach puts the creation and use of 3-D spatial grammars on a more general level and supports designers with facilitated definition and application of their own rules in a familiar computer-aided design environment without requiring programming.
A family of skeletons for motion planning and geometric reasoning applications
Authors: Eftekharian Ata A. , Ilieş Horea T.
Published: October 2011

The task of planning a path between two spatial configurations of an artifact moving among obstacles is an important problem in practically all geometrically intensive applications. Despite the ubiquity of the problem, the existing approaches make specific limiting assumptions about the geometry and mobility of the obstacles, or those of the environment in which the motion of the artifact takes place. We present a strategy to construct a family of paths, or roadmaps, for two- and three-dimensional solids moving in an evolving environment that can undergo drastic topological changes. Our approach is based on a potent paradigm for constructing geometric skeletons that relies on constructive representations of shapes with R-functions that operate on real-valued half-spaces as logic operations. We describe a family of skeletons that have the same homotopy as that of the environment and contains the medial axis as a special case. Of importance, our skeletons can be designed so that they are “attracted to” or “repulsed by” prescribed spatial sites of the environment. Moreover, the R-function formulation suggests the new concept of a medial zone, which can be thought of as a “thick” skeleton with significant applications for motion planning and other geometric reasoning applications. Our approach can handle problems in which the environment is not fully known a priori, and intrinsically supports local and parallel skeleton computations for domains with rigid or evolving boundaries. Furthermore, our path planning algorithm can be implemented in any commercial geometric kernel, and has attractive computational properties. The capability of the proposed technique are explored through several examples designed to simulate highly dynamic environments.
Functional Magnetic Resonance Imaging of Working Memory and Response Inhibition in Children with Mild Traumatic Brain Injury
Authors: Krivitzky Lauren S. , Roebuck-Spencer Tresa M. , Roth Robert M. , Blackstone Kaitlin , Johnson Chad P. , Gioia Gerard
Published: October 2011

The current pilot study examined functional magnetic resonance imaging (fMRI) activation in children with mild traumatic brain injury (mTBI) during tasks of working memory and inhibitory control, both of which are vulnerable to impairment following mTBI. Thirteen children with symptomatic mTBI and a group of controls completed a version of the Tasks of Executive Control (TEC) during fMRI scanning. Both groups showed greater prefrontal activation in response to increased working memory load. Activation patterns did not differ between groups on the working memory aspects of the task, but children with mTBI showed greater activation in the posterior cerebellum with the addition of a demand for inhibitory control. Children with mTBI showed greater impairment on symptom report and “real world” measures of executive functioning, but not on traditional “paper and pencil” tasks. Likewise, cognitive testing did not correlate significantly with imaging results, whereas increased report of post-concussive symptoms were correlated with increased cerebellar activation. Overall, results provide some evidence for the utility of symptom report as an indicator of recovery and the hypothesis that children with mTBI may experience disrupted neural circuitry during recovery. Limitations of the study included a small sample size, wide age range, and lack of in-scanner accuracy data. (JINS, 2011,17, 1143–1152)
ERM for insurance companies – adding the investor's point of view ‐ Abstract of the London Discussion
Authors: Hitchcox Andrew
Published: October 2011

This abstract relates to the following paper:

HitchcoxA.N., KlumpesP.J.M., McGaugheyK.W., SmithA.D. & TavernerN.H.ERM for insurance companies – adding the investor's point of view. British Actuarial Journal, doi:10.1017/S1357321711000122
Enhanced SUMOylation and SENP-1 Protein Levels following Oxygen and Glucose Deprivation in Neurones
Authors: Cimarosti Helena , Ashikaga Emi , Jaafari Nadia , Dearden Laura , Rubin Philip , Wilkinson Kevin A , Henley Jeremy M
Published: October 2011

Here, we show that oxygen and glucose deprivation (OGD) causes increased small ubiquitin-like modifier (SUMO)-1 and SUMO-2/3 conjugation to substrate proteins in cultured hippocampal neurones. Surprisingly, the SUMO protease SENP-1, which removes SUMO from conjugated proteins, was also increased by OGD, suggesting that the neuronal response to OGD involves a complex interplay between SUMOylation and deSUMOylation. Importantly, decreasing global SUMOylation in cultured hippocampal neurones by overexpression of the catalytic domain of SENP-1 increased neuronal vulnerability to OGD-induced cell death. Taken together, these results suggest a neuroprotective role for neuronal SUMOylation after OGD.
Situated Voices: ‘Black Women's Experience’ and Social Work
Authors: Lewis Gail
Published: October 2011

The article uses a discourse analytic approach to explore some of the ways in which black women social workers invoke the category ‘experience’ as a means by which to mediate their structural and discursive location in social services departments. The article draws on current feminist theoretical debates about ‘experience’ and the ‘multivocality’ of black women as they construct dialogic spaces with diverse interlocutors. In so doing an argument is made for an understanding of ‘black women's experience’ as constituted rather than descriptive.
Charging of a dust particle in a plasma with a non extensive electron distribution function
Authors: Tribeche Mouloud , Shukla Padma Kant
Published: October 2011

We present a theoretical model for the electrostatic charging of a spherical dust particle in an electron-ion plasma with streaming ions and a nonextensive electron distribution function following a non-Maxwell-Boltzmann law. The non-extensive electron distribution function drastically affects the electron current to dust grain surface and, therefore, the electron charge on a dust particle is significantly reduced in a non-Maxwellian dusty plasma.
MoO3 doped 4,4′-N,N′-dicarbazole-biphenyl for low voltage organic light emitting diodes
Authors: Qiu J. , Wang Z. B. , Helander M. G. , Lu Z. H.
Published: October 2011

MoO3 doped 4,4′-N,N′-dicarbazole-biphenyl (CBP) was found to provide significantly reduced driving voltage when used as a hole transport layer (HTL) in organic light emitting diodes (OLEDs). Up to 70% improvement in power efficiency was realized in a fluorescent green OLED when MoO3 doped CBP was used in place of the traditional N,N′-diphenyl-N,N′-bis-(1-naphthyl)-1-1′-biphenyl-4,4′-diamine (α-NPD) HTL. It is also found that the hole injection across the CBP:MoO3/CBP interface is dependent on the CBP:MoO3 layer thickness. Therefore, the hole injection can be engineered by tuning the doping thickness which is useful for optimizing the electron-hole balance.
An experimental and computational study of the reaction of ground-state sulfur atoms with carbon disulfide
Authors: Gao Yide , Marshall Paul
Published: October 2011

The pulsed laser photolysis/resonance fluorescence technique was used to study the reaction of S(3PJ) with CS2 in an Ar bath gas. Over 290–770 K pressure-dependent kinetics were observed and low- and high-pressure limiting rate constants were derived as k0 = (11.5–0.0133 T/K) × 10−31 cm6 molecule−2 s−1 (error limits ± 20%) and k∞ = (2.2 ± 0.6) × 10−12 cm3 molecule−1 s−1. Equilibration observed at 690–770 K yields a CS2–S bond dissociation enthalpy of 131.7 ± 4.0 kJ mol−1 at 298 K. This agrees with computed thermochemistry for a spin-forbidden C2V adduct, estimated at the coupled-cluster single double triple level extrapolated to the infinite basis set limit. A pressure-independent pathway, assigned to abstraction, was observed from 690 to 1040 K and can be summarized as 1.14 × 10−10 exp(−37.0 kJ mol−1/RT) cm3 molecule−1 s−1 with error limits of ± 40%. The results are rationalized in terms of a computed potential energy surface and transition state theory and Troe's unimolecular formalism.
Electron dynamics in two-dimensional asymmetric anti-parallel reconnection
Authors: Egedal J. , Le A. , Pritchett P. L. , Daughton W.
Published: October 2011

Kinetic simulations and spacecraft observations have documented strong anisotropy in the electron distribution function during magnetic reconnection. The level and role of electron pressure anisotropy is investigated for asymmetric geometries applicable to reconnection in the day-side magnetopause. A previously derived analytic model for the pressure anisotropy is generalized and is applied to the asymmetric geometry. In agreement with the results from a kinetic simulation, the generalized model predicts the strongest pressure anisotropy and parallel electric fields in the in-flow region characterized by low electron pressure.
Current amplification with vertical Josephson interferometers
Authors: Monaco Roberto
Published: October 2011

It has long been recognized that a control current Ia injected into the section of a two- junction superconducting quantum interference device is able to produce a change of its critical current Ic, so that a current gain g = |dIc/dIa| can be identified. We investigate the circumstances under which large gains can be achieved by using vertical Josephson interferometers, which are characterized by small loop inductances. We discuss the theory of operation of such a device, its performances, and its advantages with respect to planar interferometers used in the previous works. Two potential applications are addressed.
Influence of discharge conditions on energetic hydrogen atoms in a glow discharge
Authors: Cvetanović N. , Obradović B. M. , Kuraica M. M.
Published: October 2011

Influence of discharge conditions on fast hydrogen atoms in glow discharge is investigated using Balmer alpha emission spectroscopy. Investigation was performed in two orthogonal directions of observation in pure hydrogen. The shapes of the profiles are examined together with the space intensity distribution of the excessively broadened Balmer alpha line. It was found that line profile, space intensity distribution, and energy distribution of exited atoms strongly depend on voltage, pressure, and the reduced electric field. This confirms that fast H atoms are generated in charge exchange processes and neutralization of ions at cathode surface and not in a non-field process.
Emission spectroscopy of a microhollow cathode discharge plasma in helium-water gas mixtures
Authors: Namba S. , Yamasaki T. , Hane Y. , Fukuhara D. , Kozue K. , Takiyama K.
Published: October 2011

A dc microhollow cathode discharge (MHCD) plasma was generated inflowing helium gas containing water vapor. The cathode hole diameters were 0.3, 0.7, 1.0, and 2.0 mm, each with a length of 2.0 mm. Emission spectroscopy was carried out to investigate the discharge mode and to determine the plasma parameters. For the 0.3-mm cathode, stable MHCDs in an abnormal glow mode existed at pressures up to 100 kPa, whereas for larger diameters, a plasma was not generated at atmospheric pressure. An analysis of the lineshapes relevant to He at 667.8 nm and to Hα at 656.3 nm implied an electron density and gas temperature of 2 × 1014 cm−3 and 1100 K, respectively, for a 100-kPa discharge in the negative glow region. The dependence of the OH band, and Hα intensities on the discharge current exhibited different behaviors. Specifically, the OH spectrum had a maximum intensity at a certain current, while the H atom intensity kept increasing with the discharge current. This observation implies that a high concentration of OH radicals results in quenching, leading to the production of H atoms via the reaction OH + e− → O + H + e−.
A half-step in quantized conductance for low-density electrons in a quantum wire
Authors: Gumbs Godfrey , Balassis Antonios , Huang Danhong , Ahmed Sheehan , Brennan Ryan
Published: October 2011

We investigated the effect of perpendicular magnetic field on quantum wires when the spin-orbit interaction (SOI) of electrons is not neglected. Based on the calculated energy dispersion, the nonlinear ballistic conductance (G) and electron-diffusion thermoelectric power (Sd) are calculated as functions of the electron density, temperature and applied bias voltage. A low-temperature half-step feature in G that was observed experimentally by Quay et al. [Nat. Phys. 6, 336 (2010)], as well as a new peak in Sd are reproduced here in the low density region. These phenomena are related to the occurrence of Zeeman splitting and a SOI induced saddle point in the band structure where the channel chemical potential lies within an anticrossing gap between the saddle point of the lower subband and the bottom of the upper subband. Additionally, side peaks in G that are far away from the zero bias for the nonlinear transport, as well as a quadratic bias-voltage dependence of G near zero voltage, are predicted and discussed.
Current drive in recombining plasma
Authors: Schmit P. F. , Fisch N. J.
Published: October 2011

The Langevin equations describing the average collisional dynamics of suprathermal particles in nonstationary plasma remarkably admit an exact analytical solution in the case of recombining plasma. The current density produced by arbitrary particle fluxes is derived including the influence of charge recombination. Since recombination has the effect of lowering the charge density of the plasma, thus reducing the charged particle collisional frequencies, the evolution of the current density can be modified substantially compared to plasma with fixed charge density. The current drive efficiency is derived and optimized for discrete and continuous pulses of current, leading to the discovery of a nonzero “residual” current density that persists indefinitely under certain conditions, a feature not present in stationary plasmas.
Compressibility and hardness of Co-based bulk metallic glass: A combined experimental and density functional theory study
Authors: Wang Jianfeng , Li Ran , Xiao Ruijuan , Xu Tao , Li Yan , Liu Zengqian , Huang Lu , Hua Nengbin , Li Gong , Li Yanchun , Zhang Tao
Published: October 2011

An incompressible Co54Ta11B35 bulk metallic glass (BMG) was investigated using in situ high-pressure synchrotron diffraction and nanoindendation. The elastic constants were deduced from the experiments based on the isotropic model. The Vickers hardness was measured to be 17.1 GPa. The elastic moduli and hardness are the highest values known in BMGs. The theoretically calculated elastic properties by density-functional study were well consistent with experimental measurements. The analysis of charge density and bonding character indicates the covalent character of Co-B and B-B bonds, underlying the unusually high elastic modulus and hardness in this material.
Potential candidates for hyperhalogens: A comparative study of BO2, AlO2, and VO3 species
Authors: Pradhan Kalpataru , Jena Purusottam
Published: October 2011

Recent work has shown that BO2 which is a superhalogen with an electron affinity of 4.46 eV, can be used as building block of a new class of molecules/clusters whose electron affinities can exceed that of BO2. This class of molecules was named hyperhalogens and the concept was illustrated by focusing on Au(BO2)2. Here we explore other superhalogens besides BO2 to see if they too can be used to form hyperhalogens. We have chosen to focus on AlO2 which is valence isoelectronic with BO2 as well as VO3 which involves a transition metal atom. The results obtained using density functional theory show unexpected behavior: Although AlO2 and VO3 are both superhalogens such as BO2, only Na(BO2)2 is a hyperhalogen while Na(AlO2)2 and Na(VO3)2 are not. The origin of this anomalous result is traced to the large binding energy of the dimers of AlO2 and VO3.
Effect of wall roughness on fluid transport resistance in nanopores
Authors: Xu Baoxing , Li Yibing , Park Taehyo , Chen Xi
Published: October 2011

Using non-equilibrium molecular dynamics simulations, we investigate the effect of wall roughness on the transport resistance of water molecules inside modified carbon nanotubes. The effective shear stress, which characterizes the strong interaction between liquid molecules and solid wall, is a quantity that dominates the nanofluidic transport resistance. Both the effective shear stress and nominal viscosity arise with the increase of the amplitude or the decrease of the wavelength of roughness. The effect of roughness is also relatively more prominent in smaller nanotubes. The molecular mechanism is elucidated through the study of the radial density profile, hydrogen bonding, and velocity field of the confined water molecules.
Electrical performance of carbon nanotube-polymer composites at frequencies up to 220 GHz
Authors: Alshehri Ali H. , Jakubowska Malgorzata , Sloma Marcin , Horaczek Michal , Rudka Diana , Free Charles , David Carey J.
Published: October 2011

We have measured the sub-THz electrical response of screen printed carbon nanotube-poly(methyl methacrylate) polymer composites up to 220 GHz. The measured electrical losses using mm long coplanar waveguide geometries averaged as low as 0.15 dB/mm in the frequency range 40 GHz–110 GHz and showed a reduction in signal loss with increasing frequency; a behaviour opposite to that found in conventional metallic conductors. Between 140 and 220 GHz, the electrical losses averaged 0.28 dB/mm. We show that the low electrical losses are associated with the capacitive coupling between the nanotubes and discuss potential high frequency applications.
Effect of CdS film thickness on the photoexcited carrier lifetime of TiO2/CdS core-shell nanowires
Authors: Kumar Challa Kiran , Goswami Syamanta K. , Oh Eunsoon , Kim Eui-Tae
Published: October 2011

TiO2/CdS core-shell nanowires were synthesized using a simple thermal oxidation treatment of a Ti film, followed by O2 plasma treatment and CdS coating via low-cost chemical bath deposition. The 5 and 20 nm thick CdS films were uniformly coated onto TiO2 nanowires using 200 and 40 ml aqueous solvent, respectively. Time-resolved photoluminescence (PL) measurements on the TiO2/CdS (5 nm) nanowires showed a remarkably increased PL lifetime of 420 ps compared with the 60 ps of the TiO2/CdS (20 nm) nanowires. This result can be attributed to the enhanced electron-hole separation due to the more upshifted quantized electron energy levels of the 5 nm thick CdS film with respect to the TiO2 conduction band edge.
Magnetic properties of tris(8-hydroxyquinoline)iron: Experimental and theoretical investigation
Authors: Pang Zhiyong , Lin Liang , Wang Fenggong , Fang Shaojie , Dai Ying , Han Shenghao
Published: October 2011

The magnetic properties of tris(8-hydroxyquinoline)iron (Feq3) are investigated by experiments and first-principles density functional theory. In contrast to the diamagnetic behavior of Alq3, the Feq3 films deposited by vacuum thermal evaporating exhibit paramagnetic behaviors at 5 K. The calculated electronic structure of Feq3 molecule shows clear exchange splitting between the majority and minority spin channels. The total magnetic moment is about 1 μB, which mainly derives from the localized Fe 3d orbital. The paramagnetic behavior observed is ascribed to the small energy difference (1 meV) between ferromagnetic and antiferromagnetic coupling.
The β3-adrenergic agonist (BRL35135A) acutely increases oxygen consumption and plasma intermediate metabolites in sheep
Authors: Samadi  , Jois M. , Dunshea F. R. , Leury B. J.
Published: October 2011

There is evidence that an atypical adrenoreceptor subtype is involved in mediating some of the physiological effects of catecholamines, particularly in some adipose tissue sites. Therefore, three experiments were conducted to determine the metabolic and energetic responses to oral administration of the purported β3-agonist BRL35135A in ruminant lambs. The post-prandial increase in O2 consumption (0.109 versus 0.139 L/min) and CO2 production (0.102 versus 0.127 L/min) at 30 min after feeding was greater (P < 0.05) in the lambs receiving 5 mg of the BRL35135A. Treatment × time interactions over the period between –50 and 220 min indicate significant increases in plasma non-esterified fatty acids (P < 0.001), glucose (P < 0.001) and lactate (P = 0.024) in lambs consuming a single oral dose of 5 mg BRL35135A. In a subsequent experiment there were similar interactions over the period between –120 and 1440 min for non-esterified fatty acids (P < 0.001), glucose (P < 0.001) and lactate (P < 0.001) in lambs consuming a lower oral dose of 1 mg BRL35135A. The effects of BRL35135A on plasma non-esterified fatty acids (P = 0.95), glucose (P = 0.84) and lactate (P = 0.68) were not modified by the β1- and β2-adrenergic antagonist alprenolol suggesting that the effects were mediated via β3-adrenergic receptor subtypes. In conclusion, these experiments indicate that BRL35135A is acutely active in sheep when given with feed, as indicated by increases in respiratory gas exchange and plasma metabolite concentrations.
Is water the key? Dingo management, intraguild interactions and predator distribution around water points in arid Australia
Authors: Brawata Renee L. , Neeman Teresa
Published: October 2011

Context Predators are major beneficiaries of artificial water points in arid environments, yet little is known of the effects of water on the distribution of many sympatric species. Intraguild interactions around water points in arid Australia may play a significant role in structuring mammalian predator assemblages and influence spatial predation on some native prey species. Aims We examined how management of an apex predator, the dingo (Canis lupus dingo), influenced the distribution of two introduced mesopredators, foxes (Vulpes vulpes) and feral cats (Felis catus), around water points in arid Australia. Methods The spatial activity of dingoes, foxes and feral cats was assessed at five study sites with varying dingo management regimes. Sampling of predator activity was monitored using track counts at measured proximity to water points. Key results At sites where dingoes were uncontrolled, foxes were less likely to be found within 5 km of water points; conversely, where dingoes were controlled using exclusion fencing, fox activity was highest near water. Where dingo activity was reduced using 1080 baiting, feral cats were found closer to water. Conclusions These patterns suggest that the presence of dingoes instigates avoidance behaviour by foxes and feral cats, and through doing so may limit the use of artificial waters by these mesopredators. Through limiting access to such an essential resource in arid environments, dingoes may reduce mesopredator populations and minimise their impact on native prey. Implications For the conservation of native biodiversity, it may prove beneficial to maintain intact dingo populations due to their suppressive effect on mesopredators.
Is the relationship between predator and prey abundances related to climate for lynx and snowshoe hares?
Authors: Hone Jim , Krebs Charles J. , O'Donoghue Mark
Published: October 2011

Context
Predator dynamics may be related to prey abundance and influenced by environmental effects, such as climate. Predator–prey interactions may be represented by mechanistic models that comprise a deterministic skeleton with stochastic climatic forcing.

Aims
The aim of this study was to evaluate the effects of climate on predator–prey dynamics. The lynx and snowshoe hare predator–prey system in the Kluane region of the Yukon, Canada, is used as a case study. The specific hypothesis is that climate influences the relationship between lynx and hare abundance.

Methods
We evaluate 10 linear relationships between predator and prey abundance and effects of climate. We use data on lynx and snowshoe hare abundance over 21 years in the Yukon as the predator–prey system, and three alternative broad-scale climate indices: the winter North Atlantic Oscillation (NAO), the Pacific North American (PNA) index and the North Pacific index (NPI).

Key results
There was more support, as assessed by Akaike weights (ωi = 0.600), evidence ratio (=4.73) and R2 (=0.77) for a model of predator (lynx) and prior prey (hare) abundance with an effect of prior climate (winter NAO) when combined in a multiplicative, rather than in an additive, manner. The results infer that climate changes the amplitude of the lynx cycle with lower predator (lynx) abundance with positive values of winter NAO for a given hare density.

Conclusions
The study provides evidence that predator–prey dynamics are related to climate in an interactive manner. The ecological mechanism for the interactive effect is not clear, and alternative hypotheses are proposed for future evaluation.

Implications
The study implies that changes in climate may alter predator–prey relationships.
Entrance of the proton pathway in
cbb
3
-type heme-copper oxidases
Authors: Lee Hyun Ju , Gennis Robert B. , Ädelroth Pia
Published: October 2011

Heme-copper oxidases (HCuOs) are the last components of the respiratory chain in mitochondria and many bacteria. They catalyze O
2
reduction and couple it to the maintenance of a proton-motive force across the membrane in which they are embedded. In the mitochondrial-like, A family of HCuOs, there are two well established proton transfer pathways leading from the cytosol to the active site, the D and the K pathways. In the C family (
cbb
3
) HCuOs, recent work indicated the use of only one pathway, analogous to the K pathway. In this work, we have studied the functional importance of the suggested entry point of this pathway, the Glu-25 (
Rhodobacter sphaeroides
cbb
3
numbering) in the accessory subunit CcoP (E25
P
). We show that catalytic turnover is severely slowed in variants lacking the protonatable Glu-25. Furthermore, proton uptake from solution during oxidation of the fully reduced
cbb
3
by O
2
is specifically and severely impaired when Glu-25 was exchanged for Ala or Gln, with rate constants 100–500 times slower than in wild type. Thus, our results support the role of E25
P
as the entry point to the proton pathway in
cbb
3
and that this pathway is the main proton pathway. This is in contrast to the A-type HCuOs, where the D (and not the K) pathway is used during O
2
reduction. The
cbb
3
is in addition to O
2
reduction capable of NO reduction, an activity that was largely retained in the E25
P
variants, consistent with a scenario where NO reduction in
cbb
3
uses protons from the periplasmic side of the membrane.
Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain
Authors: Winter Michael B. , Herzik Mark A. , Kuriyan John , Marletta Michael A.
Published: October 2011

Interior topological features, such as pockets and channels, have evolved in proteins to regulate biological functions by facilitating the diffusion of biomolecules. Decades of research using the globins as model heme proteins have clearly highlighted the importance of gas pockets around the heme in controlling the capture and release of O2. However, much less is known about how ligand migration contributes to the diverse functions of other heme protein scaffolds. Heme nitric oxide/oxygen binding (H-NOX) domains are a conserved family of gas-sensing heme proteins with a divergent fold that are critical to numerous signaling pathways. Utilizing X-ray crystallography with xenon, a tunnel network has been shown to serve as a molecular pathway for ligand diffusion. Structure-guided mutagenesis results show that the tunnels have unexpected effects on gas-sensing properties in H-NOX domains. The findings provide insights on how the flux of biomolecules through protein scaffolds modulates protein chemistry.
Balancing current drive and heating in DIII-D high noninductive current fraction discharges through choice of the toroidal field
Authors: Ferron J.R. , Holcomb C.T. , Luce T.C. , Politzer P.A. , Turco F. , DeBoo J.C. , Doyle E.J. , In Y. , La Haye R.J. , Murakami M. , Okabayashi M. , Park J.M. , Petrie T.W. , Petty C.C. , Reimerdes H.
Published: October 2011

In order to maintain stationary values of the stored energy and the plasma current in a tokamak discharge with all of the current driven noninductively, the sum of the α-heating power and the power required to provide externally driven current must be equal to the power required to maintain the pressure against transport losses. In a study of high noninductive current fraction discharges in the DIII-D tokamak, it is shown that in the case of present-day tokamaks with no α-heating, adjustment of the toroidal field strength (B
T) is a tool to obtain this balance between the required current drive and heating powers with other easily modifiable discharge parameters (βN, q
95, discharge shape, n
e) fixed at values chosen to satisfy specific constraints. With all of the external power sources providing both heating and current drive, and βN and q
95 fixed, the fraction of externally driven current scales with B
T with little change in the bootstrap current fraction, thus allowing the noninductive current fraction to be adjusted.
Alteration of CFTR transmembrane span integration by disease-causing mutations
Authors: Patrick Anna E. , Karamyshev Andrey L. , Millen Linda , Thomas Philip J.
Published: October 2011

Many missense mutations in the cystic fibrosis transmembrane conductance regulator protein (CFTR) result in its misfolding, endoplasmic reticulum (ER) accumulation, and, thus, cystic fibrosis. A number of these mutations are located in the predicted CFTR transmembrane (TM) spans and have been projected to alter span integration. However, the boundaries of the spans have not been precisely defined experimentally. In this study, the ER luminal integration profiles of TM1 and TM2 were determined using the ER glycosylation machinery, and the effects of the CF-causing mutations G85E and G91R thereon were assessed. The mutations either destabilize the integrated conformation or alter the TM1 ER integration profile. G85E misfolding is based in TM1 destabilization by glutamic acid and loss of glycine and correlates with the temperature-insensitive ER accumulation of immature full-length CFTR harboring the mutation. By contrast, temperature-dependent misfolding owing to the G91R mutation depends on the introduction of the basic side chain rather than the loss of the glycine. This work demonstrates that CF-causing mutations predicted to have similar effects on CFTR structure actually result in disparate molecular perturbations that underlie ER accumulation and the pathology of CF.
Hook2 is involved in the morphogenesis of the primary cilium
Authors: Baron Gaillard Carole L. , Pallesi-Pocachard Emilie , Massey-Harroche Dominique , Richard Fabrice , Arsanto Jean-Pierre , Chauvin Jean-Paul , Lecine Patrick , Krämer Helmut , Borg Jean-Paul , Le Bivic André
Published: October 2011

Primary cilia originate from the centrosome and play essential roles in several cellular, developmental, and pathological processes, but the underlying mechanisms of ciliogenesis are not fully understood. Given the involvement of the adaptor protein Hook2 in centrosomal homeostasis and protein transport to pericentrosomal aggresomes, we explored its role in ciliogenesis. We found that in human retinal epithelial cells, Hook2 localizes at the Golgi apparatus and centrosome/basal body, a strategic partitioning for ciliogenesis. Of importance, Hook2 depletion disrupts ciliogenesis at a stage before the formation of the ciliary vesicle at the distal tip of the mother centriole. Using two hybrid and immunoprecipitation assays and a small interfering RNA strategy, we found that Hook2 interacts with and stabilizes pericentriolar material protein 1 (PCM1), which was reported to be essential for the recruitment of Rab8a, a GTPase that is believed to be crucial for membrane transport to the primary cilium. Of interest, GFP::Rab8a coimmunoprecipitates with endogenous Hook2 and PCM1. Finally, GFP::Rab8a can overcome Hook2 depletion, demonstrating a functional interaction between Hook2 and these two important regulators of ciliogenesis. The data indicate that Hook2 interacts with PCM1 in a complex that also contains Rab8a and regulates a limiting step required for further initiation of ciliogenesis after centriole maturation.
Gathering insights on disease etiology from gene expression profiles of healthy tissues
Authors: Silva A. Sofia , Wood Shona H. , van Dam Sipko , Berres Sven , McArdle Anne , de Magalhães João Pedro
Published: October 2011

Motivation: Gene expression profiles have been widely used to study disease states. It may be possible, however, to gather insights into human diseases by comparing gene expression profiles of healthy organs with different disease incidence or severity. We tested this hypothesis and developed an approach to identify candidate genes associated with disease development by focusing on cancer incidence since it varies greatly across human organs.

Results: We normalized organ-specific cancer incidence by organ weight and found that reproductive organs tend to have a higher mass-normalized cancer incidence, which could be due to evolutionary trade-offs. Next, we performed a genome-wide scan to identify genes whose expression across healthy organs correlates with organ-specific cancer incidence. We identified a large number of genes, including genes previously associated with tumorigenesis and new candidate genes. Most genes exhibiting a positive correlation with cancer incidence were related to ribosomal and transcriptional activity, translation and protein synthesis. Organs with enhanced transcriptional and translational activation may have higher cell proliferation and therefore be more likely to develop cancer. Furthermore, we found that organs with lower cancer incidence tend to express lower levels of known cancer-associated genes. Overall, these results demonstrate how genes and processes that predispose organs to specific diseases can be identified using gene expression profiles from healthy tissues. Our approach can be applied to other diseases and serve as foundation for further oncogenomic analyses.

Contact:  jp@senescence.info

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Crop and Non-Crop Plants as Potential Reservoir Hosts of Alfalfa mosaic virus and Cucumber mosaic virus for Spread to Commercial Snap Bean
Authors: Mueller E. E. , Groves R. L. , Gratton C.
Published: October 2011

Diseases caused by aphid-transmitted viruses such as Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV) have increased in snap bean (Phaseolus vulgaris) in the Midwestern United States. Plants immediately surrounding agricultural fields may serve as primary virus inocula for aphids to acquire and transmit to bean crops. The project objectives were to (i) identify potentially important AMV and CMV reservoirs among naturally infected plants and (ii) determine the relationship between the virus inoculum potential (VIP) in adjacent crop field margins and virus incidence in P. vulgaris. From 2006 to 2008, surveys were conducted to quantify the virus incidence and percentage cover (2008 only) of plants present within 5 m of the P. vulgaris crop. In all, 4,350 individual plants representing 44 species were assayed, with overall AMV and CMV incidences averaging 12 and 1.5%, respectively. A VIP index was developed and used to rank the importance of virus-susceptible plants in adjacent field margins. The overall VIP index for AMV in field margins was weakly associated with AMV incidence in P. vulgaris and no relationship was observed between local CMV inoculum and P. vulgaris incidence, suggesting that factors additional to local inoculum sources may influence CMV epidemics in P. vulgaris.
Identification of New Pathogenic Races of Common Bunt and Dwarf Bunt Fungi, and Evaluation of Known Races Using an Expanded Set of Differential Wheat Lines
Authors: Goates Blair J.
Published: October 2011

Pathogenic races of Tilletia caries and T. foetida, which cause common bunt of wheat (Triticum aestivum), and Tilletia contraversa, which causes dwarf bunt of wheat, have been identified previously by their reaction to 10 differential wheat lines, each containing single bunt resistance genes Bt1 through Bt10. The reactions of races to the differential wheat lines follow the classic gene-for gene system for host–pathogen interactions. The pathogens are closely related and resistance to both diseases in wheat is controlled by the same genes. To better define pathogenic races, six additional wheat lines containing the genes Bt11 through Bt15 and a wheat line with a resistance factor designated as Btp were added to the set of 10 differentials and tested with all named U.S. races of common bunt and dwarf bunt. In addition, new isolates of dwarf bunt, and common bunt from hybrids and field collections, were tested with all 16 differentials for race identification. Six new races of T. caries, five new races of T. foetida, and two new races of T. contraversa were identified. Races of common bunt virulent to Bt8 or Bt12, and dwarf bunt races virulent to the combinations of Bt11 and Bt12, and Bt8, Bt9, Bt10, Bt11, and Bt12, were identified for the first time. Comparison of the reactions of the common bunt races with the Bt14 and Bt15 differentials grown in different environments after initial infection showed that these genes are temperature sensitive, indicating they should be excluded from the set of differential lines to avoid ambiguity in determining virulent or avirulent reactions. In the previous list of bunt races, there were races that had the same reaction to the set of 10 differentials but were designated as different races. These races were not differentiated further with the six additional differentials, indicating that the duplicate races should be dropped from the list of pathogenic races. The new races of common bunt and dwarf bunt identified have unique patterns of virulence that allow specific targeting and elucidation of bunt resistance genes in wheat and will aid the development of bunt-resistant wheat cultivars.
Influence of strontium for calcium substitution in bioactive glasses on degradation, ion release and apatite formation
Authors: Fredholm Yann C. , Karpukhina Natalia , Brauer Delia S. , Jones Julian R. , Law Robert V. , Hill Robert G.
Published: October 2011

Bioactive glasses are able to bond to bone through the formation of hydroxy-carbonate apatite in body fluids while strontium (Sr)-releasing bioactive glasses are of interest for patients suffering from osteoporosis, as Sr was shown to increase bone formation both
in vitro
and
in vivo
. A melt-derived glass series (SiO
2
–P
2
O
5
–CaO–Na
2
O) with 0–100% of calcium (Ca) replaced by Sr on a molar base was prepared. pH change, ion release and apatite formation during immersion of glass powder in simulated body fluid and Tris buffer at 37°C over up to 8 h were investigated and showed that substituting Sr for Ca increased glass dissolution and ion release, an effect owing to an expansion of the glass network caused by the larger ionic radius of Sr ions compared with Ca. Sr release increased linearly with Sr substitution, and apatite formation was enhanced significantly in the fully Sr-substituted glass, which allowed for enhanced osteoblast attachment as well as proliferation and control of osteoblast and osteoclast activity as shown previously. Studying the composition–structure–property relationship in bioactive glasses enables us to successfully design next-generation biomaterials that combine the bone regenerative properties of bioactive glasses with the release of therapeutically active Sr ions.
Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches
Authors: Tuffery Pierre , Derreumaux Philippe
Published: October 2011

The recognition process between a protein and a partner represents a significant theoretical challenge.In silicostructure-based drug design carried out with nothing more than the three-dimensional structure of the protein has led to the introduction of many compounds into clinical trials and numerous drug approvals. Central to guiding the discovery process is to recognize active among non-active compounds. While large-scale computer simulations of compounds taken from a library (virtual screening) or designed de novo are highly desirable in the post-genomic area, many technical problems remain to be adequately addressed. This article presents an overview and discusses the limits of current computational methods for predicting the correct binding pose and accurate binding affinity. It also presents the performances of the most popular algorithms for exploring binary and multi-body protein interactions.
Analysis of subcellular G3BP redistribution during rubella virus infection
Authors: Matthews Jason D. , Frey Teryl K.
Published: October 2011

Rubella virus (RUBV) replicates slowly and to low titre in vertebrate cultured cells, with minimal cytopathology. To determine whether a cellular stress response is induced during such an infection, the formation of Ras-GAP-SH3 domain-binding protein (G3BP)-containing stress granules (SGs) in RUBV-infected cells was examined. Late in infection, accumulation of G3BP granules was detected, albeit in fewer than half of infected cells. Active virus RNA replication was required for induction of these granules, but they were found to differ from SGs induced by arsenite treatment both in composition (they did not uniformly contain other SG proteins, such as PABP and TIA-1) and in resistance to cycloheximide treatment. Thus, bona fide SGs do not appear to be induced during RUBV infection. The distribution of G3BP, either on its own or in granules, did not overlap with that of dsRNA-containing replication complexes, indicating that it played no role in virus RNA synthesis. However, G3BP did co-localize with viral ssRNAs in perinuclear clusters, suggesting an interaction that could possibly be important in a post-replicative role in virus replication, such as encapsidation.
Estimation of rearrangement phylogeny for cancer genomes
Authors: Greenman Chris D. , Pleasance Erin D. , Newman Scott , Yang Fengtang , Fu Beiyuan , Nik-Zainal Serena , Jones David , Lau King Wai , Carter Nigel , Edwards Paul A.W. , Futreal P. Andrew , Stratton Michael R. , Campbell Peter J.
Published: October 2011

Cancer genomes are complex, carrying thousands of somatic mutations including base substitutions, insertions and deletions, rearrangements, and copy number changes that have been acquired over decades. Recently, technologies have been introduced that allow generation of high-resolution, comprehensive catalogs of somatic alterations in cancer genomes. However, analyses of these data sets generally do not indicate the order in which mutations have occurred, or the resulting karyotype. Here, we introduce a mathematical framework that begins to address this problem. By using samples with accurate data sets, we can reconstruct relatively complex temporal sequences of rearrangements and provide an assembly of genomic segments into digital karyotypes. For cancer genes mutated in rearranged regions, this information can provide a chronological examination of the selective events that have taken place.
HDA6 Directly Interacts with DNA Methyltransferase MET1 and Maintains Transposable Element Silencing in Arabidopsis
Authors: Liu Xuncheng , Yu Chun-Wei , Duan Jun , Luo Ming , Wang Koching , Tian Gang , Cui Yuhai , Wu Keqiang
Published: October 2011

The molecular mechanism of how the histone deacetylase HDA6 participates in maintaining transposable element (TE) silencing in Arabidopsis (Arabidopsis thaliana) is not yet defined. In this study, we show that a subset of TEs was transcriptionally reactivated and that TE reactivation was associated with elevated histone H3 and H4 acetylation as well as increased H3K4Me3 and H3K4Me2 in hda6 mutants. Decreased DNA methylation of the TEs was also detected in hda6 mutants, suggesting that HDA6 silences the TEs by regulating histone acetylation and methylation as well as the DNA methylation status of the TEs. Similarly, transcripts of some of these TEs were also increased in the methyltransferase1 (met1) mutant, with decreased DNA methylation. Furthermore, H4 acetylation, H3K4Me3, H3K4Me2, and H3K36Me2 were enriched at the coregulated TEs in the met1 and hda6 met1 mutants. Protein-protein interaction analysis indicated that HDA6 physically interacts with MET1 in vitro and in vivo, and further deletion analysis demonstrated that the carboxyl-terminal region of HDA6 and the bromo-adjacent homology domain of MET1 were responsible for the interaction. These results suggested that HDA6 and MET1 interact directly and act together to silence TEs by modulating DNA methylation, histone acetylation, and histone methylation status.
Using the Judas technique to locate and remove wintertime aggregations of invasive common carp
Authors: BAJER P. G. , CHIZINSKI C. J. , SORENSEN P. W.
Published: October 2011

Abstract  Radio‐ and acoustic telemetry in three Midwestern lakes demonstrated that common carp, Cyprinus carpio L., aggregate as water temperatures descend below 10 °C. Particularly dense aggregations formed at temperatures <5 °C, and once located, these aggregations could be removed with an efficiency of up to 94% using seine nets. Carp aggregated just below the surface of the ice (approximately 1.5 m) and rarely descended to warmer waters, which extended down to 10 m. Although aggregations consistently formed close to shore, their locations could not be explained by temperature or dissolved oxygen. The aggregations also moved frequently, making radio‐tagged fish invaluable to locate them. Coldwater aggregations of carp may reflect a type of shoaling behaviour and can be exploited with the aid of radio‐tagged (Judas) fish to control this invasive fish effectively. Similar approaches might be developed for other gregarious invasive fishes.