bluuebunny/crossref_metadata_2025 huggingface dataset:
An auroral oval at the footprint of Saturn's kilometric radio sources, colocated with the UV aurorae
Authors: Lamy L. , Cecconi B. , Prangé R. , Zarka P. , Nichols J. D. , Clarke J. T.
Published: October 2009

Similarly to other magnetized planets, Saturn displays auroral emissions generated by accelerated electrons gyrating around high‐latitude magnetic field lines. They mainly divide in ultraviolet (UV) and infrared (IR) aurorae, excited by electron collisions with the upper atmosphere, and Saturn's kilometric radiation (SKR), radiated from higher altitudes by electron‐wave resonance. Whereas spatially resolved UV and IR images of atmospheric aurorae reveal a continuous auroral oval around each pole, the SKR source locus was only indirectly constrained by the Voyager radio experiment to a limited local time (LT) range on the morningside, leading to interpretation of the SKR modulation as a fixed flashing light. Here, we present resolved SKR maps derived from the Cassini Radio and Plasma Wave Science (RPWS) experiment using goniopolarimetric techniques. We observe radio sources all around the planet, organized along a high‐latitude continuous auroral oval. Observations of the Hubble Space Telescope obtained in January 2004 and January 2007 have been compared to simultaneous and averaged Cassini‐RPWS measurements, revealing that SKR and UV auroral ovals are very similar, both significantly enhanced on the dawnside. These results imply that the SKR and atmospheric aurorae are triggered by the same populations of energetic electron beams, requiring a unified model of particle acceleration and precipitation on Saturn.
Role of the tropical Atlantic sea surface temperature in the decadal change of the summer North Atlantic Oscillation
Authors: Sun Jianqi , Wang Huijun , Yuan Wei
Published: October 2009

Recent observational studies have shown that the southern center of the summer North Atlantic Oscillation (SNAO) shifted eastward after the late 1970s. In this study, this phenomenon and its causes are further explored. It is found that the decadal spatial shift of the SNAO southern center is related to the decadal variability of the tropical Atlantic sea surface temperature (TASST). In the past half century, the TASST experienced an abrupt change around the late 1970s, with a rapid warming in the recent 2 decades. Thus in the period after the late 1970s when the TASST is relatively warmer, the TASST released more energy into the atmosphere, then stimulated strong convection over the tropical Atlantic, and further excited anomalous wave‐like patterns. This strengthened the circulation in the region of the Mediterranean Sea, namely the east part of the SNAO southern center, consequently leading to an eastward shift of the SNAO southern center. Meanwhile, in the period before the late 1970s when the TASST is relatively cooler, the TASST released less energy into the atmosphere, so its impact on the overlying atmosphere was significantly weakened and confined to the lower‐level atmosphere of the tropical Atlantic. Thus the TASST possibly did not influence the variability of the SNAO southern center, and the SNAO pattern exhibited a traditional distribution with two centers over the North Atlantic.
Wild-type and missense mutants of retinoschisin co-assemble resulting in either intracellular retention or incorrect assembly of the functionally active octamer
Authors: Gleghorn Lindsay J. , Trump Dorothy , Bulleid Neil J.
Published: October 2009

The X-linked disease retinoschisis is caused by mutations in the RS1 gene encoding retinoschisin, most commonly missense mutations leading to a lack of secretion of functional protein. One potential approach to treat this disease would be the introduction of the wild-type protein by gene therapy in affected individuals. Retinoschisin normally forms homo-octamers, so co-expression of the wild-type protein with the mutant could result in their co-assembly. In the present study, we show that retinoschisin assembles into an octamer before transport from the endoplasmic reticulum and that co-assembly of wild-type and mutant protein can occur when they are co-expressed in the same cell. This co-assembly results in the retention of some, but not all, expressed wild-type retinoschisin. Moreover, when the wild-type protein is expressed with a missense mutant that is normally secreted, co-assembly occurs resulting in the secretion of a heterogeneous mixture of oligomers. Missense mutations of retinoschisin which cause intracellular retention also lead to an unfolded protein response. However, this is not sufficient to decrease cell viability suggesting that the pathology of the disease is not likely to be linked to programmed cell death.
The molecular basis of the effect of temperature on enzyme activity
Authors: Daniel Roy M. , Peterson Michelle E. , Danson Michael J. , Price Nicholas C. , Kelly Sharon M. , Monk Colin R. , Weinberg Cristina S. , Oudshoorn Matthew L. , Lee Charles K.
Published: October 2009

Experimental data show that the effect of temperature on enzymes cannot be adequately explained in terms of a two-state model based on increases in activity and denaturation. The Equilibrium Model provides a quantitative explanation of enzyme thermal behaviour under reaction conditions by introducing an inactive (but not denatured) intermediate in rapid equilibrium with the active form. The temperature midpoint (Teq) of the rapid equilibration between the two forms is related to the growth temperature of the organism, and the enthalpy of the equilibrium (ΔHeq) to its ability to function over various temperature ranges. In the present study, we show that the difference between the active and inactive forms is at the enzyme active site. The results reveal an apparently universal mechanism, independent of enzyme reaction or structure, based at or near the active site, by which enzymes lose activity as temperature rises, as opposed to denaturation which is global. Results show that activity losses below Teq may lead to significant errors in the determination of ΔG*cat made on the basis of the two-state (‘Classical’) model, and the measured kcat will then not be a true indication of an enzyme's catalytic power. Overall, the results provide a molecular rationale for observations that the active site tends to be more flexible than the enzyme as a whole, and that activity losses precede denaturation, and provide a general explanation in molecular terms for the effect of temperature on enzyme activity.
Tunable steady-state domain wall oscillator with perpendicular magnetic anisotropy
Authors: Bisig A. , Heyne L. , Boulle O. , Kläui M.
Published: October 2009

We theoretically study domain wall oscillations upon the injection of a dc current through a geometrically constrained wire with perpendicular magnetic anisotropy. The frequency spectrum of the oscillation can be tuned by the injected current density and additionally by the application of an external magnetic field. Our analytical calculations are supported by micromagnetic simulations based on the Landau–Lifshitz–Gilbert equation. The simple concept of our localized steady-state oscillator might prove useful as a nanoscale microwave generator with possible applications in telecommunications or for rf-assisted writing in magnetic hard drives.
Temporal and spatial resolved optical emission behaviors of a cold atmospheric pressure plasma jet
Authors: Xiong Q. , Lu X. , Liu J. , Xian Y. , Xiong Z. , Zou F. , Zou C. , Gong W. , Hu J. , Chen K. , Pei X. , Jiang Z. , Pan Y.
Published: October 2009

The propagation behavior of cold atmospheric pressure plasma jets has recently attracted lots of attention. In this paper, a cold He plasma jet generated by a single plasma electrode jet device is studied. The spatial-temporal resolved optical emission spectroscopy measurements are presented. It is found that the emission intensity of the He 706.5 nm line of the plasma behaves similarly both inside the syringe and in the surrounding air (plasma plume). It decreases monotonously, which is different from the emission lines, such as N2 337.1 nm line, N2+ 391.4 nm line, and O 777.3 nm line. For the discharge inside the syringe, the emission intensity of the He 706.5 nm line decays more rapidly than that of the other three spectral lines mentioned above. The N2 337.1 nm line behaves a similar time evolution with the discharge current. For the N2+ 391.4 nm line and the atomic O 777.3 nm line, both of them decay slower than that of the He 706.5 nm and the N2 337.1 nm. When the plasma plume propagates further away from the nozzle, the temporal behaviors of the emission intensities of the four lines tend to be similar gradually. Besides, it is found that, when the size of the plasma bullet appears biggest, the propagation velocity of the bullet achieves its highest value while the emission intensity of the N2+ 391.4 nm line reaches its maximum. Detailed analysis shows that the Penning effect between the metastable state Hem and the air molecules may play a significant role in the propagation of the plasma bullet in the open air.
Amorphous composition in Gd–Co–Al system extracted from bulk metallic glass matrix composite
Authors: Fu H. , Guo M. S. , Yu H. J. , Zu X. T. , Liu M.
Published: October 2009

Multiphase structure including the metallic glass matrix and the primary crystalline phase(s) was found in the Gd55Co15Al30−xGex (0≤x≤10) alloys. It was confirmed by x-ray diffraction and energy dispersive spectroscopy that the primary crystalline phase was Gd5Ge3 when x≥5. Based on these results, ternary bulk metallic glasses with composition of Gd52.5–53.8Co16.5–20.5Al25.7–31.0, which exhibit good glass forming ability and high thermal stability, were discovered.
A considerable metamagnetic shape memory effect without any prestrain in Ni46Cu4Mn38Sn12 Heusler alloy
Authors: Li Z. , Jing C. , Zhang H. L. , Qiao Y. F. , Cao S. X. , Zhang J. C. , Sun L.
Published: October 2009

Spontaneous strains during martensitic transformation and magnetic-field-induced transformation have been systemically studied for Ni46Cu4Mn38Sn12 Heusler alloy, respectively. A large spontaneous strain with the value of about 0.12% upon martensitic transformation has been observed in this alloy, which is almost three times larger than that in ternary Ni–Mn–Sn alloy. In addition, such a value of strain can be obtained through a fully reverse martensitic transformation induced by a field of about 45 kOe, exhibiting a considerable metamagnetic shape memory effect without any prestrain. This behavior can be attributed to magnetoelastic coupling between stable martensite and metastable fraction of austenite.
Velocity map imaging using an in-vacuum pixel detector
Authors: Gademann Georg , Huismans Ymkje , Gijsbertsen Arjan , Jungmann Julia , Visschers Jan , Vrakking Marc J. J.
Published: October 2009

The use of a new type in-vacuum pixel detector in velocity map imaging (VMI) is introduced. The Medipix2 and Timepix semiconductor pixel detectors (256×256 square pixels, 55×55 μm2) are well suited for charged particle detection. They offer high resolution, low noise, and high quantum efficiency. The Medipix2 chip allows double energy discrimination by offering a low and a high energy threshold. The Timepix detector allows to record the incidence time of a particle with a temporal resolution of 10 ns and a dynamic range of 160 μs. Results of the first time application of the Medipix2 detector to VMI are presented, investigating the quantum efficiency as well as the possibility to operate at increased background pressure in the vacuum chamber.
The effect of interbranch spacing on structural and rheological properties of hyperbranched polymer melts
Authors: Le Tu C. , Todd B. D. , Daivis P. J. , Uhlherr A.
Published: October 2009

Nonequilibrium molecular dynamics simulations were performed for a family of hyperbranched polymers of the same molecular weight but with different chain lengths between branches. Microscopic structural properties including mean squared radius of gyration, distribution of beads from the center of mass and from the core and the interpenetration function of these systems were characterized. A relationship between the zero shear rate mean squared radius of gyration and the Wiener index was established. The molecular and bond alignment tensors were analyzed to characterize the flow birefringence of these hyperbranched polymers. The melt rheology was also studied and the crossover from the Newtonian to non-Newtonian behavior was captured for all polymer fluids in the considered range of strain rates. Rheological properties including the shear viscosity and normal stress coefficients obtained from constant pressure simulations were found to be the same as those from constant volume simulations except at high strain rates due to shear dilatancy. A linear dependence of zero shear rate viscosities on the number of spacer units was found. The stress optical rule was shown to be valid at low strain rates with the stress optical coefficient of approximately 3.2 independent of the topologies of polymers.
Retarding field energy analyzer for the Saskatchewan Torus–Modified plasma boundary
Authors: Dreval M. , Rohraff D. , Xiao C. , Hirose A.
Published: October 2009

The retarding field energy analyzer (RFA) is a simple and reliable diagnostic technique to measure the ion temperature in the scrape-off layer and edge of magnetic fusion devices. Design and operation features of a single-sided (facing the ion flow) RFA for ion temperature measurements in the Saskatchewan Torus–Modified (STOR-M) tokamak are described. Its compact size (21×15×20 mm3) allows RFA measurements without perturbing plasma significantly. Both ion and electron temperature have been measured by RFA in the STOR-M tokamak. A method is proposed to correct the effects of ion flow on the ion temperature using the simultaneously measured Mach number. The measured electron temperature is consistent with the previously reported Langmuir probe data. Abnormal behavior of the RFA has been observed in both ion and electron modes when RFA is inserted deep into the plasma.
Phase partitioning and site-preference of hafnium in the γ′(L12)∕γ(fcc) system in Ni-based superalloys: An atom-probe tomographic and first-principles study
Authors: Amouyal Yaron , Mao Zugang , Seidman David N.
Published: October 2009

Atom-probe tomography (APT) and first-principles calculations are employed to investigate the partitioning of Hf in the γ′(L12)∕γ(fcc) phases in two multicomponent Ni-based superalloys. APT results indicate strong partitioning of Hf atoms to the γ(fcc)-phase. We perform first-principles calculations of the substitutional formation energy of Hf for a model γ(Ni)∕γ′(Ni3Al) system indicating Hf partitioning to the γ′-phase. Additional calculations of the Hf–Cr binding energy suggest, however, that Cr atoms, which partition to the γ-phase, have a strong attractive binding energy with Hf atoms, thus predicting a reversal of the Hf partitioning in favor of the γ-phase due to alloying with Cr.
Accurate ab initio energy gradients in chemical compound space
Authors: Anatole von Lilienfeld O.
Published: October 2009

Analytical potential energy derivatives, based on the Hellmann–Feynman theorem, are presented for any pair of isoelectronic compounds. Since energies are not necessarily monotonic functions between compounds, these derivatives can fail to predict the right trends of the effect of alchemical mutation. However, quantitative estimates without additional self-consistency calculations can be made when the Hellmann–Feynman derivative is multiplied with a linearization coefficient that is obtained from a reference pair of compounds. These results suggest that accurate predictions can be made regarding any molecule’s energetic properties as long as energies and gradients of three other molecules have been provided. The linearization coefficent can be interpreted as a quantitative measure of chemical similarity. Presented numerical evidence includes predictions of electronic eigenvalues of saturated and aromatic molecular hydrocarbons.
Gigahertz breathing oscillators based on carbon nanoscrolls
Authors: Shi Xinghua , Pugno Nicola M. , Cheng Yuan , Gao Huajian
Published: October 2009

Theoretical study and molecular dynamics simulations are performed to investigate the gigahertz “breathing” oscillatory motion of a carbon nanoscroll (CNS). It is shown that the oscillation frequency depends on surface energy, bending stiffness, interlayer spacing, and length of the basal graphene sheet of the CNS, and that energy dissipation in the system can be controlled by adjusting temperature, graphene length, and surface energy. The analysis indicates potential applications of CNS in nanomechanical devices such as nanooscillators, nanoactuators, as well as drug and gene delivery systems.
Effect of uniaxial-strain on Ge p-i-n photodiodes integrated on Si
Authors: Yu Hyun-Yong , Kim Donghyun , Ren Shen , Kobayashi Masaharu , Miller David A. B. , Nishi Yoshio , Saraswat Krishna C.
Published: October 2009

We demonstrate the effect of uniaxial tensile and compressive strain in Ge p-i-n photodiode integrated on Si using four-point bending structures. Responsivity at 1550 nm is increased from 0.67 to 0.75 A/W by tensile strain in the ⟨110⟩ direction while for compressive strain it decreases from 0.67 to 0.477 A/W. These uniaxial tensile and compressive strains also effectively result in shifts of the absorption spectra toward longer and shorter wavelength as they reduce or increase the direct bandgap energy of the Ge layer, respectively.
Composition and concentration anomalies for structure and dynamics of Gaussian-core mixtures
Authors: Pond Mark J. , Krekelberg William P. , Shen Vincent K. , Errington Jeffrey R. , Truskett Thomas M.
Published: October 2009

We report molecular dynamics simulation results for two-component fluid mixtures of Gaussian-core particles, focusing on how tracer diffusivities and static pair correlations depend on temperature, particle concentration, and composition. At low particle concentrations, these systems behave like simple atomic mixtures. However, for intermediate concentrations, the single-particle dynamics of the two species largely decouple, giving rise to the following anomalous trends. Increasing either the concentration of the fluid (at fixed composition) or the mole fraction of the larger particles (at fixed particle concentration) enhances the tracer diffusivity of the larger particles but decreases that of the smaller particles. In fact, at sufficiently high particle concentrations, the larger particles exhibit higher mobility than the smaller particles. Each of these dynamic behaviors is accompanied by a corresponding structural trend that characterizes how either concentration or composition affects the strength of the static pair correlations. Specifically, the dynamic trends observed here are consistent with a single empirical scaling law that relates an appropriately normalized tracer diffusivity to its pair-correlation contribution to the excess entropy.
Genetic ablation of retinal pigment epithelial cells reveals the adaptive response of the epithelium and impact on photoreceptors
Authors: Longbottom Rebecca , Fruttiger Marcus , Douglas Ron H. , Martinez-Barbera Juan Pedro , Greenwood John , Moss Stephen E.
Published: October 2009

The retinal pigment epithelium (RPE) plays a critical role in the maintenance of the outer retina. RPE cell death or dysfunction drives the pathophysiology of many retinal diseases, but the physiological response of the retina to RPE cell loss is poorly understood, mainly because of the absence of suitable experimental models. Here, we generated a transgenic mouse in which an inducible Cre recombinase is expressed exclusively in the RPE under the control of the monocarboxylate transporter 3 gene promoter (RPE
CreER
). This was crossed with a transgenic mouse harboring a diphtheria toxin A (DTA) chain gene rendered transcriptionally silent by a floxed stop sequence. We show that activation of DTA in the double transgenic mouse (RPE
CreER
/DTA) led to 60–80% RPE cell death, with surviving cells maintaining the integrity of the monolayer by increasing their size. Despite the apparent morphological normality of the enlarged RPE cells in the RPE
CreER
/DTA mice, functional analysis revealed significant deficits on electroretinography, and retinal histopathology showed regions of photoreceptor rosetting and degeneration although with retention of a normal vascular network. Our study reveals that whilst the RPE monolayer has a remarkable intrinsic capacity to cope with cellular attrition, specific aspects of RPE multifunctionality essential for photoreceptor survival are compromised. The RPE
CreER
/DTA mouse offers advantages over models that employ chemical or mechanical strategies to kill RPE cells, and should be useful for the development and evaluation of RPE-based therapies, such as stem cell transplantation.
Spatiotemporally separable
Shh
domains in the midbrain define distinct dopaminergic progenitor pools
Authors: Joksimovic Milan , Anderegg Angela , Roy Anil , Campochiaro Laura , Yun Beth , Kittappa Raja , McKay Ronald , Awatramani Rajeshwar
Published: October 2009

Midbrain dopamine neurons (mDA) are important regulators of diverse physiological functions, including movement, attention, and reward behaviors. Accordingly, aberrant function of dopamine neurons underlies a wide spectrum of disorders, such as Parkinson's disease (PD), dystonia, and schizophrenia. The distinct functions of the dopamine system are carried out by neuroanatomically discrete subgroups of dopamine neurons, which differ in gene expression, axonal projections, and susceptibility in PD. The developmental underpinnings of this heterogeneity are undefined. We have recently shown that in the embryonic CNS, mDA originate from the midbrain floor plate, a ventral midline structure that is operationally defined by the expression of the molecule Shh. Here, we develop these findings to reveal that in the embryonic midbrain, the spatiotemporally dynamic
Shh
domain defines multiple progenitor pools. We deduce 3 distinct progenitor pools, medial, intermediate, and lateral, which contribute to different mDA clusters. The earliest progenitors to express
Shh
, here referred to as the medial pool, contributes neurons to the rostral linear nucleus and mDA of the ventral tegmental area/interfascicular regions, but remarkably, little to the substantia nigra pars compacta. The intermediate
Shh
+ progenitors give rise to neurons of all dopaminergic nuclei, including the SNpc. The last and lateral pool of
Shh
+ progenitors generates a cohort that populates the red nucleus, Edinger Westphal nucleus, and supraoculomotor nucleus and cap. Subsequently, these lateral
Shh
+ progenitors produce mDA. This refined ontogenetic definition will expand understanding of dopamine neuron biology and selective susceptibility, and will impact stem cell-derived therapies and models for PD.
Hotspots of GPI-anchored proteins and integrin nanoclusters function as nucleation sites for cell adhesion
Authors: van Zanten Thomas S. , Cambi Alessandra , Koopman Marjolein , Joosten Ben , Figdor Carl G. , Garcia-Parajo Maria F.
Published: October 2009

Recruitment of receptor proteins to lipid rafts has been proposed as an important mechanism to regulate their cellular function. In particular, rafts have been implicated in regulation of integrin-mediated cell adhesion, although the underlying mechanism remains elusive. We used single-molecule near-field optical microscopy (NSOM) with localization accuracy of approximately 3 nm, to capture the spatio-functional relationship between the integrin LFA-1 and raft components (GPI-APs) on immune cells. Dual color nanoscale imaging revealed the existence of a nanodomain GPI-AP subpopulation that further concentrated in regions smaller than 250 nm, suggesting a hierarchical prearrangement of GPI-APs on resting monocytes. We previously demonstrated that in quiescent monocytes, LFA-1 preorganizes in nanoclusters. We now show that integrin nanoclusters are spatially different but reside proximal to GPI-AP nanodomains, forming hotspots on the cell surface. Ligand-mediated integrin activation resulted in an interconversion from monomers to nanodomains of GPI-APs and the generation of nascent adhesion sites where integrin and GPI-APs colocalized at the nanoscale. Cholesterol depletion significantly affected the reciprocal distribution pattern of LFA-1 and GPI-APs in the resting state, and LFA-1 adhesion to its ligand. As such, our data demonstrate the existence of nanoplatforms as essential intermediates in nascent cell adhesion. Since raft association with a variety of membrane proteins other than LFA-1 has been documented, we propose that hotspots regions enriched with raft components and functional receptors may constitute a prototype of nanoscale inter-receptor assembly and correspond to a generic mechanism to offer cells with privileged areas for rapid cellular function and responses to the outside world.
Interaction of an autotransporter passenger domain with BamA during its translocation across the bacterial outer membrane
Authors: Ieva Raffaele , Bernstein Harris D.
Published: October 2009

Autotransporters are a superfamily of virulence factors produced by Gram-negative bacteria consisting of a large N-terminal extracellular domain (“passenger domain”) and a C-terminal β barrel domain (“β domain”). The mechanism by which the passenger domain is translocated across the outer membrane (OM) is unknown. Here we show that the insertion of a small linker into the passenger domain of the
Escherichia coli
O157:H7 autotransporter EspP effectively creates a translocation intermediate by transiently stalling translocation near the site of the insertion. Using a site-specific photocrosslinking approach, we found that residues adjacent to the stall point interact with BamA, a component of a heterooligomeric complex (Bam complex) that catalyzes OM protein assembly, and that residues closer to the EspP N terminus interact with the periplasmic chaperones SurA and Skp. The EspP–BamA interaction was short-lived and could be detected only when passenger domain translocation was stalled. These results support a model in which molecular chaperones prevent misfolding of the passenger domain before its secretion and the Bam complex catalyzes both the integration of the β domain into the OM and the translocation of the passenger domain across the OM in a C- to N-terminal direction.
Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry
Authors: Chetty Palaniappan Sevugan , Mayne Leland , Lund-Katz Sissel , Stranz David , Englander S. Walter , Phillips Michael C.
Published: October 2009

Apolipoprotein A-I (apoA-I) stabilizes anti-atherogenic high density lipoprotein particles (HDL) in the circulation and governs their biogenesis, metabolism, and functional interactions. To decipher these important structure–function relationships, it will be necessary to understand the structure, stability, and plasticity of the apoA-I molecule. Biophysical studies show that lipid-free apoA-I contains a large amount of α-helical structure but the location of this structure and its properties are not established. We used hydrogen-deuterium exchange coupled with a fragmentation-separation method and mass spectrometric analysis to study human lipid-free apoA-I in its physiologically pertinent monomeric form. The acquisition of ≈100 overlapping peptide fragments that redundantly cover the 243-residue apoA-I polypeptide made it possible to define the positions and stabilities of helical segments and to draw inferences about their interactions and dynamic properties. Residues 7–44, 54–65, 70–78, 81–115, and 147–178 form α-helices, accounting for a helical content of 48 ± 3%, in agreement with circular dichroism measurements (49%). At 3 to 5 kcal/mol in free energy of stabilization, the helices are far more stable than could be achieved in isolation, indicating mutually stabilizing helix bundle interactions. However the helical structure is dynamic, unfolding and refolding in seconds, allowing facile apoA-I reorganization during HDL particle formation and remodeling.
Myocardin is required for cardiomyocyte survival and maintenance of heart function
Authors: Huang Jianhe , Min Lu Min , Cheng Lan , Yuan Li-Jun , Zhu Xiaoquing , Stout Andrea L. , Chen Mary , Li Jian , Parmacek Michael S.
Published: October 2009

Despite intense investigation over the past century, the molecular mechanisms that regulate maintenance and adaptation of the heart during postnatal development are poorly understood. Myocardin is a remarkably potent transcriptional coactivator expressed exclusively in cardiac myocytes and smooth muscle cells during postnatal development. Here we show that myocardin is required for maintenance of cardiomyocyte structure and sarcomeric organization and that cell-autonomous loss of myocardin in cardiac myocytes triggers programmed cell death. Mice harboring a cardiomyocyte-restricted null mutation in the myocardin gene (
Myocd
) develop dilated cardiomyopathy and succumb from heart failure within a year. Remarkably, ablation of the
Myocd
gene in the adult heart leads to the rapid-onset of heart failure, dilated cardiomyopathy, and death within a week.
Myocd
gene ablation is accompanied by dissolution of sarcomeric organization, disruption of the intercalated disc, and cell-autonomous loss of cardiomyocytes via apoptosis. Expression of myocardin/serum response factor-regulated myofibrillar genes is extinguished, or profoundly attenuated, in myocardin-deficient hearts. Conversely, proapoptotic factors are induced and activated in myocardin-deficient hearts. We conclude that the transcriptional coactivator myocardin is required for maintenance of heart function and ultimately cardiomyocyte survival.
During its nuclear phase the multifunctional regulatory protein ICP0 undergoes proteolytic cleavage characteristic of polyproteins
Authors: Gu Haidong , Poon Alice P. , Roizman Bernard
Published: October 2009

ICP0 is a multifunctional herpes simplex virus protein known primarily as a promiscuous transactivator. In the course of productive infection, it is localized during the first 5–7 h in the nucleus and later in the cytoplasm. In the nucleus, its primary activities are to suppress the silencing of viral DNA by host proteins, activate cdk4 through recruitment of cyclin D3 to the sites of formation of replication compartments, and degrade several cellular proteins including PML and Sp100, key components of the ND10 nuclear bodies. ICP0 is not translocated to the cytoplasm in cells infected with mutants incapable of performing these tasks. We report the unexpected finding that ICP0 is cleaved into several discrete polypeptides by a proteasome-independent process. The products of this cleavage accumulate in cells infected with ICP0 mutants incapable of degrading PML and therefore are retained in the nucleus. In the second step, the products of the initial cleavage of wild-type virus-infected cells are themselves subject to proteasome-dependent degradation. The average half life of intact ICP0 during the nuclear phase is approximately 1 h. The proteasome-independent cleavage products are no longer detected at late times corresponding to the cytoplasmic phase of ICP0. The results are consistent with the hypothesis that the cleavage products of ICP0 function in topologically distinct domains during its nuclear phase.
Risk Factors for Mortality in Patients with NosocomialStenotrophomonas maltophiliaPneumonia
Authors: Tseng Chia-Cheng , Fang Wen-Feng , Huang Kuo-Tung , Chang Pei-Wen , Tu Mei-Lien , Shiang Yi-Ping , Douglas I. S. , Lin Meng-Chih
Published: October 2009

Objective.

The aim of this study was to determine potential risk factors for mortality in patients with nosocomialStenotrophomonas maltophiliapneumonia.

Design.

A retrospective, single-center, observational study.

Setting.

A 2400-bed tertiary teaching hospital in southern Taiwan.

Patients and Methods.

This retrospective study evaluated patients (age, at least 18 years) with nosocomial pneumonia (S. maltophiliaisolated from respiratory culture) who were seen at Kaohsiung Chang Gung Memorial Hospital over a 3-year period. A total of 406 patients (64% male, mean age ± standard deviation, 69.6 ± 14.93 years; mean duration of hospital stay ± standard deviation, 57.5 ± 39.47 days) were included.

Results.

Most index isolates (53.9%) were from the first sample cultured. Polymicrobial isolates were cultured from samples from 177 (43.6%) of the 406 study patients. The most common copathogen wasPseudomonas aeruginosa(53.11% of isolates). The all-cause hospital mortality rate was 42.6% (173 deaths among 406 patients). Survivors had a shorter time from admission to a positive index culture result than did nonsurvivors (26.1 vs 31.7 days;P= .04). Mortality was significantly higher among patients with malignancy (adjusted odds ratio [AOR], 2.48; 95% confidence interval [CI], 1.52–4.07;P< .001 ), renal disease (AOR, 2.6; 95% CI, 1.51–4.47;P= .001), intensive care unit stay (AOR, 1.72; 95% CI, 1.1–2.7;P= .018), and inadequate initial empirical antibiotic therapy (AOR, 2.17; 95% CI, 1.4–3.38;P= .001).

Conclusions.

S. maltophiliapneumonia is associated with a high mortality rate and is commonly associated with concomitant polymicrobial colonization or infection. Underlying comorbidities and inadequate initial empirical antibiotic therapy substantially account for increased mortality rates.
Wave-front dividing beam combined laser fusion driver using stimulated Brillouin scattering phase conjugation mirrors
Authors: Kong H.J. , Shin J.S. , Yoon J.W. , Beak D.H.
Published: October 2009

The beam combination method using stimulated Brillouin scattering phase conjugation mirrors (SBS-PCMs) is a promising technique for a commercial laser fusion driver operated with a high repetition rate around 10 Hz. The phase control of the SBS wave is essential for realization of the coherent beam combined output in the beam combination. For this reason, we proposed the ‘self-phase control technique’ of the stimulated Brillouin scattering wave, and its principle has been demonstrated experimentally over the past several years. In this work, the experiments are performed for the phase stabilization of wave-front dividing two-beam and four-beam combined systems by reducing the beam pointing fluctuation of the laser source using a beam expansion.
Ancestors 1.0: a web server for ancestral sequence reconstruction
Authors: Diallo Abdoulaye Banire , Makarenkov Vladimir , Blanchette Mathieu
Published: October 2009

Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.

Availability: The Ancestors 1.0 is available at http://ancestors.bioinfo.uqam.ca/ancestorWeb/.

Contact:  diallo.abdoulaye@uqam.ca
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D
Authors: Niu Yun , Otasek David , Jurisica Igor
Published: October 2009

Motivation: Identification and characterization of protein–protein interactions (PPIs) is one of the key aims in biological research. While previous research in text mining has made substantial progress in automatic PPI detection from literature, the need to improve the precision and recall of the process remains. More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction.

Results: We developed an interaction detection method and explored the usefulness of various features in automatically identifying PPIs in text. The results show that our approach outperforms other systems using the AImed dataset. In the tests where our system achieves better precision with reduced recall, we discuss possible approaches for improvement. In addition to test datasets, we evaluated the performance on interactions from five human-curated databases—BIND, DIP, HPRD, IntAct and MINT—where our system consistently identified evidence for ∼60% of interactions when both proteins appear in at least one sentence in the PubMed abstract. We then applied the system to extract articles from PubMed to annotate known, high-throughput and interologous interactions in I2D.

Availability: The data and software are available at: http://www.cs.utoronto.ca/∼juris/data/BI09/.

Contact:  yniu@uhnres.utoronto.ca; juris@ai.utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method
Authors: Ma Shuangge , Zhang Yawei , Huang Jian , Han Xuesong , Holford Theodore , Lan Qing , Rothman Nathaniel , Boyle Peter , Zheng Tongzhang
Published: October 2009

Motivation: Although NHL (non-Hodgkin's lymphoma) is the fifth leading cause of cancer incidence and mortality in the USA, it remains poorly understood and is largely incurable. Biomedical studies have shown that genomic variations, measured with SNPs (single nucleotide polymorphisms) in genes, may have independent predictive power for disease-free survival in NHL patients beyond clinical measurements.

Results: We apply the CTGDR (clustering threshold gradient directed regularization) method to genetic association studies using SNPs, analyze data from an association study of NHL and identify prognosis signatures to diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most common subtypes of NHL. With the CTGDR method, we are able to account for the joint effects of multiple genes/SNPs, whereas most existing studies are single-marker based. In addition, we are able to account for the ‘gene and SNP-within-gene’ hierarchical structure and identify not only predictive genes but also predictive SNPs within identified genes. In contrast, existing studies are limited to either gene or SNP identification, but not both. We propose using resampling methods to evaluate the predictive power and reproducibility of identified genes and SNPs. Simulation study and data analysis suggest satisfactory performance of the CTGDR method.

Contact:  shuangge.ma@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Neural mechanisms for learned birdsong
Authors: Mooney Richard
Published: October 2009

Learning by imitation is essential for transmitting many aspects of human culture, including speech, language, art, and music. How the human brain enables imitation remains a mystery, but the underlying neural mechanisms must harness sensory feedback to adaptively modify performance in reference to the object of imitation. Although examples of imitative learning in nonhuman animals are relatively rare, juvenile songbirds learn to sing by copying the song of an adult tutor. The delineation of neural circuits for birdsong raises the promise that this complex form of vocal learning, which bears strong parallels to human speech learning, can be understood in terms of underlying neural mechanisms. This promise is now being more fully realized, with recent experimental advances leading to better understanding of the central motor codes for song and the central mechanisms by which auditory experience modifies song motor commands to enable vocal learning.
A summit of cladistics: abstracts of the 27th Annual Meeting of the Willi Hennig Society and VIII Reunión Argentina de Cladística y Biogeografía
Authors: Szumik Claudia , Goloboff Pablo
Published: October 2009

The 27th meeting of the Willi Hennig Society was held at the Sierras de San Javier, Tucumán (27–31 October 2008), jointly with the VIII Reunión Argentina de Cladística y Biogeografía. This was the second Hennig meeting held in South America and the third in Latin America. The event was attended by 129 participants from 16 countries, with the strongest presence from Argentina, USA and Brazil. As pointed out in the minutes of previous meetings, student participation is a good measure of the health of a society, and by this measure, the Hennig society is doing very well. For this meeting, 64 of the participants (50%) were students, 40 of which had authored or co‐authored a talk or poster. The schedule was intense, with 98 presentations (67 talks and 31 posters). The sessions consisted of contributed papers, and five symposia on diverse topics: Large Scale Analyses of Large Chunks of Life, Molecular Systematics, Latin American Biogeography in the 21st Century, Methodology, and Botanical Phylogenetics (each of the symposia, except the “green” one, had two or three student speakers). As is usual at these meetings, the atmosphere was informal and relaxed, with much discussion and debate (although the biogeographic symposium took first place for the heat of its exchanges). The Student Award Committee (Lone Aagesen, Dan Janies and Gitte Petersen) selected Santiago Catalano for the Hennig Award (‘The optimization of landmark data: a three‐dimensional approach’), Prashant Sharma for the Brundin Award (‘Phylogenetic analysis of Sandokanidae (Arachnida, Opiliones, Laniatores): Evaluating the independence of associated gene regions’), and Sebastian Barrionuevo for the Rosen Award (‘Continuous characters in a phylogenetic analysis of the frog genus Telmatobius’). In addition to the logistics and funding provided by the Willi Hennig Society, the event was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas, Fundación Miguel Lillo, Instituto Superior de Entomología ‘Dr Abraham Willink’, and the Agencia Nacional de Promoción Científica y Tecnológica. © The Willi Hennig Society 2009.
Phylogeny, biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini based on morphological and molecular characters (Coleoptera: Staphylinidae: Aleocharinae)
Authors: Ahn Kee‐Jeong , Jeon Mi‐Jeong , Branham Marc A.
Published: October 2009

A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325–355 bp), and nearly complete sequences of 18S rDNA (1768–1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus,Ianmoorea) (Paramblopusa((Amblopusa,Halorhadinus) (Liparocephalus,Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genusParamblopusaand clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high‐ to mid‐tide zones.

 © The Willi Hennig Society 2009.
Novel human papillomavirus type 18 replicon and its application in screening the antiviral effects of cytokines
Authors: Satsuka Ayano , Yoshida Satoshi , Kajitani Naoko , Nakamura Hiroyasu , Sakai Hiroyuki
Published: October 2009

Human papillomaviruses (HPVs) infect the stratified epithelial organ. The infection induces benign tumors, which occasionally progress into malignant tumors. To elucidate the virus‐induced tumorigenesis, an understanding of the lifecycle of HPV is crucial. In this report, we developed a new system for the analysis of the HPV lifecycle. The new system consists of a novel HPV replicon and an organotypic “raft” culture, by which the HPV‐DNA is maintained stably in normal human keratinocytes for a long period and the viral vegetative replication is reproduced. This system will benefit biochemical and genetic studies on the lifecycle of HPV and tumorigenesis. This system is also valuable in screening for antiviral compounds. We confirmed its usefulness by evaluating the antivirus effect of cytokines. (Cancer Sci 2009 00: 000–000)
Observations on the breeding behaviour of the Stripe‐breasted tit (Parus fasciiventer) in Bwindi Impenetrable National Park, Uganda
Authors: Yatuha Jane , Dranzoa Christine
Published: October 2009

The motivation of this study was to investigate some hitherto unknown information on the breeding ecology of the Stripe‐breasted Tit (Parus fasciiventer) in Bwindi Impenetrable National Park, south‐western Uganda. Parus fasciiventer is one of the least studied and endemic bird species restricted to the montane forests of the Albertine Rift. Regionally, it is classified as near‐threatened. The study was carried out around the Institute of Tropical Forest Conservation Ruhija camp and the period of study was from January to June 2003. Data were generated through direct observation at the nest box sites of three active nests. Each of the nest boxes was monitored from the time of nest building to the time the chicks fledged. Results and comparative assessments from this study demonstrate that P. fasciiventer, compared with its temperate congeners like Great Tits (Parus major), Marsh Tits (Parus palustris), Crested Tits (Parus cristatus), Coal Tits (Parus ater) and Blue Tits (Parus caeruleus), raised small broods and had longer nestling period. The findings further revealed that the species is capable of raising more than one brood in a single breeding season and provide further evidence that it is a cooperative breeder. Parents participated equally in raising the young, an indication of pure parenting in the species.