bluuebunny/crossref_metadata_2025 huggingface dataset:
Core ionization of Na+ microsolvated in water and ammonia
Authors: Kryzhevoi Nikolai V. , Cederbaum Lorenz S.
Published: February 2009

Microsolvation of ions is a subject of active explorations pursuing the objectives of understanding microscopic details of ion solvation in bulk solutions. In the present work core ionization of positively charged microsolvated clusters is addressed. This research area did not receive much attention so far. The Na 1s−1 core ionization spectra of Na+(H2O)n and Na+(NH3)n clusters have been calculated by means of an accurate ab initio Green’s function method. Various dependencies of the core ionization energy on the number of solvent molecules, their arrangement, and chemical type are investigated and explained. Special emphasis is also given to the low-energy parts of the calculated core ionization spectra that exhibit numerous shake-up satellites mostly originating from the transfer of electrons from the solvent molecules to the Na+ ion induced by core ionization. Spectral characteristics of selected charge-transfer satellites are discussed in detail.
Protein adsorption on heterogeneous surfaces
Authors: Aggarwal Nitesh , Lawson Ken , Kershaw Matthew , Horvath Robert , Ramsden Jeremy
Published: February 2009

The adsorption of the protein bovine serum albumin from an aqueous solution onto substrata made from pure silica, pure zirconia, and a mixture of the two has revealed that the adsorption behavior of the protein onto the mixture very significantly diverges from the corresponding mean of the behaviors with the pure substrata. A tentative explanation in terms of matching substratum heterogeneity with protein surface heterogeneity is offered.
Electron charging in epitaxial Ge quantum dots on Si(100)
Authors: Ketharanathan Sutharsan , Sinha Sourabh , Shumway John , Drucker Jeff
Published: February 2009

Electron confinement to heteroepitaxial Ge/Si(100) quantum dots encapsulated in a Si matrix was investigated using capacitance-voltage measurements. Optimized growth conditions produced dot ensembles comprised of either huts and pyramids or dome clusters allowing investigation of electron confinement to these distinct dot morphologies. At room temperature, 20–40 nm diameter hut and pyramid clusters confine ∼0.7 electrons, while 60–80 nm diameter dome clusters confine ∼6 electrons. The greater capacity of dome clusters may be attributed to the four distinct conduction band minima that are deeper than the single minimum found for pyramid clusters using a simple band structure model.
Optical bistability enhanced by highly localized bulk plasmon polariton modes in subwavelength metal-nonlinear dielectric multilayer structure
Authors: Chen Junxue , Wang Pei , Wang Xiaolei , Lu Yonghua , Zheng RongSheng , Ming Hai , Zhan Qiwen
Published: February 2009

Optical bistability of subwavelength metal-nonlinear dielectric multilayer structure is numerically studied in this letter. It is found that very low intensity thresholds for optical bistability can be achieved due to the excitation of highly localized bulk plasmon polariton modes with TM polarized illumination. A bistability threshold of 6.9 MW/cm2 is obtained for BPP0 mode, which is much lower than the recently reported results based on the large local field enhancement at the band edge of metal-dielectric photonic band gap structure [A. Husakou and J. Herrmann, Phys. Rev. Lett. 99, 127402 (2007)].
Impact of boron-interstitial clusters on Hall scattering factor in high-dose boron-implanted ultrashallow junctions
Authors: Severac Fabrice , Cristiano Fuccio , Bedel-Pereira Elena , Fazzini Pier Francesco , Lerch Wilfried , Paul Silke , Hebras Xavier , Giannazzo Filippo
Published: February 2009

The Hall scattering factor rH has been determined for holes in high-dose boron-implanted ultrashallow junctions containing high concentrations of boron-interstitial clusters (BICs), combining scanning capacitance microscopy, nanospreading resistance, Hall effect, and secondary ion mass spectroscopy measurements. A value of rH=0.74±0.1 has been found in reference defect-free fully activated junctions, in good agreement with the existing literature. In the case of junctions containing high concentrations of immobile and electrically inactive BICs, and independently of the implant or the annealing process, the rH value has been found to be equal to 0.95±0.1. The increase in the rH value is explained in terms of the additional scattering centers associated to the presence of high concentrations of BICs.
Material functions of liquid n-hexadecane under steady shear via nonequilibrium molecular dynamics simulations: Temperature, pressure, and density effects
Authors: Tseng Huan-Chang , Wu Jiann-Shing , Chang Rong-Yeu
Published: February 2009

Computer experiments of rheology regarding the effects of temperature (T), pressure (P), and density (ρ) on steady shear flow material functions, which include viscosity (η) and first and second normal stress coefficients (ψ1 and ψ2) depending on shear rate (γ̇), have been conducted via nonequilibrium molecular dynamics simulations for liquid n-hexadecane. Straightforwardly, using both characteristic values of a zero-shear-rate viscosity and critical shear rate, η-γ̇ flow curves are well normalized to achieve the temperature-, pressure-, and density-invariant master curves, which can be formulary described by the Carreau–Yasuda rheological constitutive equation. Variations in the rate of shear thinning, obviously exhibiting in η-γ̇, ψ1-γ̇, and −ψ2-γ̇ relationships, under different T, P, and ρ values, are concretely revealed through the power-law model’s exponent. More importantly, at low shear rates, the fluid explicitly possesses Newtonian fluidic characteristics according to both manifestations; first and second normal stress differences decay to near zero, while nonequilibrium states are close to equilibrium ones. Significantly, the tendency to vary of the degree of shear thinning in rheology is qualitatively contrary to that of shear dilatancy in thermodynamics. In addition, a convergent transition point is evidently observed in the −ψ2/ψ1-γ̇ curves undergoing dramatic variations, which should be associated with shear dilatancy, as addressed analytically.
Dielectrical properties of metal-insulator-metal aluminum nitride structures: Measurement and modeling
Authors: Ben Hassine Nizar , Mercier Denis , Renaux Philippe , Parat Guy , Basrour Skandar , Waltz Patrice , Chappaz Cédrick , Ancey Pascal , Blonkowski Serge
Published: February 2009

The electrical properties of polycrystalline aluminum nitride (AlN) films grown by reactive dc magnetron sputtering are investigated in the transient and the steady-state regimes through metal-insulator-metal (MIM) structures with molybdenum (Mo) as metal electrodes. Measurements of current-time, current-voltage, and current-temperature characteristics are performed on AlN MIM structures. The extracted dielectric constant is 9.9. The transient current is observed to follow the empirical Curie–Von Schweidler law and its dependence on the applied field and the operating temperature is modeled. The time approach result is compared with the frequency-approach result by measuring the permittivity dispersion for low frequencies. Also, all the leakage mechanisms in AlN are identified in the steady-state regime depending on the applied field range. For a low electric field, the conduction mechanism is the Ohmic regime and the AlN resistivity is estimated to be 2.1×1015 Ω cm at room temperature. For higher electric fields, the ionic conduction is observed to be the dominant mechanism while the Poole–Frenkel transport is identified in the breakdown (BD) vicinity. A statistical approach is used to study the BD strength of the AlN through the Weibull distribution. The critical field for the dielectric BD ranges from 4.64 to 5.84 MV cm−1.
Electrical properties of PbTe doped with BaF2
Authors: Mengui U. A. , Abramof E. , Rappl P. H. O. , Díaz B. , Closs H. , Senna J. R. , Ueta A. Y.
Published: February 2009

We study here the p-type doping of PbTe with BaF2. For the investigation, PbTe layers were grown on (111) BaF2 substrates by molecular beam epitaxy. The beam flux ratio between BaF2 and PbTe, defined as the nominal doping level, was varied from 0.02% to 1%. The hole density increases from 5×1017 to 1×1019 cm−3 as the doping level rises from 0.02% to 0.4% and saturates at p∼1019 cm−3 for higher levels. The saturation effect was attributed to self-compensation. The carrier concentration of all samples remained almost constant as the temperature was varied from 10 to 350 K, indicating that no thermal activation is present in the whole doping range. It suggests that the impurity level in PbTe doped with BaF2 remains resonant with the valence band, similar to the native defects behavior. The low-temperature mobility showed a pronounced reduction from 50 000 to 2 000 cm2/V s as the doping level rises from 0.02% to 1%, mainly due to the substantial increase in the hole concentration. For temperatures higher than 80 K, the mobility was essentially limited by phonon scattering. Our results demonstrate that a controlled p-type doping of PbTe with BaF2 can be obtained up to 1019 cm−3.
Characteristics of nanosecond pulse needle-to-plane discharges at high pressure: a particle-in-cell Monte Carlo collision simulation
Authors: Sang Chaofeng , Sun Jizhong , Ren Chunsheng , Wang Dezhen
Published: February 2009

A model of one dimensional in position and three dimensional in velocity space self-consistent particle in cell with Monte Carlo collision technique was employed to simulate the argon discharge between the needle and plane electrodes at high pressure, in which a nanosecond rectangular pulse was applied to the needle electrode. The work focused on the investigation of the spatiotemporal evolution of the discharge versus the needle tip size and working gas pressure. The simulation results showed that the discharge occurred mainly in the region near the needle tip at atmospheric pressure, and that the small radius of the needle tip led to easy discharge. Reducing the gas pressure gave rise to a transition from a corona discharge to a glowlike discharge along the needle-to-plane direction. The microscopic mechanism for the transition can arguably be attributed to the peak of high-energy electrons occurring before the breakdown; the magnitude of the number of these electrons determined whether the breakdown can take place.
Surface morphology and electronic structure of bulk single crystal β-Ga2O3(100)
Authors: Lovejoy T. C. , Yitamben E. N. , Shamir N. , Morales J. , Villora E. G. , Shimamura K. , Zheng S. , Ohuchi F. S. , Olmstead M. A.
Published: February 2009

Experimental studies of the surface morphology and electronic structure of bulk single crystals of the transparent and wide gap semiconductor gallium oxide (β-Ga2O3) have been conducted using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and angle-resolved photoemission spectroscopy (ARPES). Atomically resolved STM and LEED results for the β-Ga2O3(100) surface clarify that the predominant surface termination contains both gallium and oxygen, and this surface does not exhibit a reconstruction. The valence band structure was obtained with ARPES and shows good agreement with existing theoretical works at the zone center and along the a∗ and c∗ directions, except that the calculated bandwidth is ∼7% too small. There is poorer agreement along the b∗ direction, where the experimental bands disperse more strongly than the calculations.
Ideal dipole approximation fails to predict electronic coupling and energy transfer between semiconducting single-wall carbon nanotubes
Authors: Wong Cathy Y. , Curutchet Carles , Tretiak Sergei , Scholes Gregory D.
Published: February 2009

The electronic coupling values and approximate energy transfer rates between semiconductor single-wall carbon nanotubes are calculated using two different approximations, the point dipole approximation and the distributed transition monopole approximation, and the results are compared. It is shown that the point dipole approximation fails dramatically at tube separations typically found in nanotube bundles (∼12–16 Å) and that the disagreement persists at large tube separations (>100 Å, over ten nanotube diameters). When used in Förster resonance energy transfer theory, the coupling between two point transition dipoles is found to overestimate energy transfer rates. It is concluded that the point dipole approximation is inappropriate for use with elongated systems such as carbon nanotubes and that methods which can account for the shape of the particle are more suitable.
Optical transmission properties of perforated metal films in the middle-infrared range
Authors: Ye Yong-Hong , Cao Yurong , Wang Zhi-Bing , Yan Desheng , Zhang Jia-Yu
Published: February 2009

We experimentally studied the enhanced optical transmission of perforated silver films in the middle-infrared region. The optical transmission properties of the samples with classical inductive frequency selective surface structures are also affected by both the periodicity and the aperture shape. Our results indicate that the physical operating mechanisms are the same for the plasmon crystal and the frequency selective surface, and both surface plasmon polaritons due to the periodicity and waveguide modes that are present in single holes have effect in the optical transmission enhancement.
Mechanism of particle removal by megasonic waves
Authors: Kim Wonjung , Kim Tae-Hong , Choi Jaehyuck , Kim Ho-Young
Published: February 2009

We elucidate the major mechanism of microparticle removal in the megasonic cleaning process through the direct visualization experiments. It is revealed that particles sitting on solids are removed by adjacent microbubbles that oscillate near the substrates and exert interfacial and pressure gradient forces on the particles. Other pressure and streaming effects are shown to be too weak to detach the particles.
Proton-exchanged OH− absorption spectra of highly Zn-doped LiNbO3 with and without polarization inversion
Authors: Tsai Pei-Chang , Chia Chih-Ta , Lin Shou-Tai , Huang Yen-Chieh , Lu Hsiu-Feng , Lin Sheng-Hsien
Published: February 2009

The proton-exchanged OH− absorption spectra of congruent and 8.1 mol % Zn-doped LiNbO3 single crystals with and without polarization inversion are presented. The variation in the proton-exchanged OH− spectra for the congruent sample is not affected by polarization inversion. This result confirms the Li-vacancy model. However, the highly doped sample shows stronger increase in intensities with polarization inversion. In our investigation, highly negative charge vacancy model confirms with proton-exchanged OH− absorption spectra and domain inversion etching experiment. Finally, we demonstrated the polarization inversion mechanism with these two samples based on extended x-ray-absorption fine structure experimental results.
Scotopic Foveal Afterimages
Authors: Hubel David H , Howe Piers D L , Duffy Amanda M , Hernández Adriana
Published: February 2009

If, after being in the dark for many minutes, one views an extended surface under dim (scotopic) illumination, one fails to see any hint of the dark spot at the center of gaze that might be expected from the absence of rods in the fovea. Here we report that, if the surface is suddenly completely darkened, one sees for a few seconds a relatively bright spot, about 2 deg in size, at the point of fixation. If the surface is now restored to its original brightness, a dark spot of similar size appears where one fixates, that again lasts for several seconds. All this can be observed with no elaborate apparatus.
Grasping Partly Occluded Objects: Effects of Global Stimulus Information on Action
Authors: Lommertzen Janneke , van Lier Rob , Meulenbroek Ruud G J
Published: February 2009

We investigated here how partly occluded stimuli affect early and late prehension kinematics. Stimuli were pictures of partly occluded cylindrical objects with indentations or protrusions at regular intervals along the contour. They diverged into two plausible completions: a local completion, comprising a linear continuation of the contour, and a global completion, revealing a continuation of the contour indentations. Convergent stimuli with one plausible completion acted as controls. Twenty-eight participants repeatedly performed a grasping movement in darkness, as if they grasped the earlier-seen partly occluded cylinder. The peak acceleration of the hand opening (occurring at about 20% of the movement time) and the maximum hand aperture (at about 60% of the movement time) were taken to reflect the representation of the width of the stimuli used for action. The results show that the grasping movements were affected not only by local but also by global stimulus properties of which the representation remained stable over time.
A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis
Authors: Lin Shuangjun , Van Lanen Steven G. , Shen Ben
Published: February 2009

Nonribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of many biologically active peptides and typically are modular, with each extension module minimally consisting of a condensation, an adenylation, and a peptidyl carrier protein domain responsible for incorporation of an amino acid into the growing peptide chain. C-1027 is a chromoprotein antitumor antibiotic whose enediyne chromophore consists of an enediyne core, a deoxy aminosugar, a benzoxazolinate, and a β-amino acid moiety. Bioinformatics analysis suggested that the activation and incorporation of the β-amino acid moiety into C-1027 follows an NRPS mechanism whereby biosynthetic intermediates are tethered to the peptidyl carrier protein SgcC2. Here, we report the biochemical characterization of SgcC5, an NRPS condensation enzyme that catalyzes ester bond formation between the SgcC2-tethered (
S
)-3-chloro-5-hydroxy-β-tyrosine and (
R
)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core. SgcC5 uses (
S
)-3-chloro-5-hydroxy-β-tyrosyl-SgcC2 as the donor substrate and exhibits regiospecificity for the C-2 hydroxyl group of the enediyne core mimic as the acceptor substrate. Remarkably, SgcC5 is also capable of catalyzing amide bond formation, albeit with significantly reduced efficiency, between (
S
)-3-chloro-5-hydroxy-β-tyrosyl-(
S
)-SgcC2 and (
R
)-2-amino-1-phenyl-1-ethanol, an alternative enediyne core mimic bearing an amine at its C-2 position. Thus, SgcC5 is capable of catalyzing both ester and amide bond formation, providing an evolutionary link between amide- and ester-forming condensation enzymes.
Exploring the roles of noise in the eukaryotic cell cycle
Authors: Kar Sandip , Baumann William T. , Paul Mark R. , Tyson John J.
Published: February 2009

The DNA replication–division cycle of eukaryotic cells is controlled by a complex network of regulatory proteins, called cyclin-dependent kinases, and their activators and inhibitors. Although comprehensive and accurate deterministic models of the control system are available for yeast cells, reliable stochastic simulations have not been carried out because the full reaction network has yet to be expressed in terms of elementary reaction steps. As a first step in this direction, we present a simplified version of the control system that is suitable for exact stochastic simulation of intrinsic noise caused by molecular fluctuations and extrinsic noise because of unequal division. The model is consistent with many characteristic features of noisy cell cycle progression in yeast populations, including the observation that mRNAs are present in very low abundance (≈1 mRNA molecule per cell for each expressed gene). For the control system to operate reliably at such low mRNA levels, some specific mRNAs in our model must have very short half-lives (<1 min). If these mRNA molecules are longer-lived (perhaps 2 min), then the intrinsic noise in our simulations is too large, and there must be some additional noise suppression mechanisms at work in cells.
Correlation signature of the macroscopic states of the gene regulatory network in cancer
Authors: Slavov Nikolai , Dawson Kenneth A.
Published: February 2009

Although cancer types differ substantially, many cancers share common gene expression signatures. Consistent with this observation, we find convergent and representative distributions and correlation vectors that are distinct in cancer and noncancer ensembles. These differences originate in many genes, but comparatively few genes account for the major differences. We identify genes with different combinatorial regulation in cancer and noncancer as indicated by significant differences in their correlation vectors. Among the identified genes are many established oncogenes and apoptotic genes (such as members of the Bcl-2, the MAPK, and the Ras families) and new candidate oncogenes. Our findings expand and complement the tumorigenic role of up and down regulation of these genes by emphasizing cancer-specific changes in their couplings and correlation patterns at genome-wide level that are independent from their mean levels of expression in cancer cells. Given the central role of these genes in defining the cancerous state it may be worth investigating them and the differences in their combinatorial regulation for developing wide-spectrum anticancer drugs.
Photoperiod alters autonomic regulation of the heart
Authors: Weil Zachary M. , Norman Greg J. , DeVries A. Courtney , Berntson Gary G. , Nelson Randy J.
Published: February 2009

Outside of the tropics, environmental conditions fluctuate in a generally predictable manner across the year. Many small mammals have evolved mechanisms, such as seasonal breeding and annual adjustments in physiology, morphology, and behavior, that promote winter survival when food is scarce and thermoregulation is challenging. Photoperiod (day length) is a cue used by many seasonal breeders to predict seasonal changes in environmental conditions. One system that is uniquely situated to mediate photoperiod-induced alterations in physiology is the autonomic nervous system (ANS). The 2 branches of the ANS are key regulators of immune responses, thermoregulation, and energy balance, functions that undergo marked shifts in baseline and reactivity following acclimation to short day lengths. Although previous studies have investigated the effects of photoperiod on ANS endpoints, this study examined the direct effects of photoperiod on integrated ANS function. To test the hypothesis that short day lengths increase parasympathetic and sympathetic tones, we maintained adult male Siberian hamsters (
Phodopus sungorus
) to either long or short photoperiods and then analyzed electrocardiogram recordings. Short day lengths increased both parasympathetic tone, as measured by respiratory sinus arrhythmia, and sympathetic control of the heart, measured with autonomic blockade. Additionally, short day lengths enhanced the withdrawal of parasympathetic control and the increase of sympathetic tone in response to acute restraint stress. Finally, these effects were discovered to be independent of circulating androgens. These data indicate that the ANS of Siberian hamsters undergoes profound changes following prolonged exposure to short winter-like day lengths.
Selective loss of GABA
B
receptors in orexin-producing neurons results in disrupted sleep/wakefulness architecture
Authors: Matsuki Taizo , Nomiyama Mika , Takahira Hitomi , Hirashima Noriko , Kunita Satoshi , Takahashi Satoru , Yagami Ken-ichi , Kilduff Thomas S. , Bettler Bernhard , Yanagisawa Masashi , Sakurai Takeshi
Published: February 2009

Hypothalamic neurons that contain the neuropeptide orexin (hypocretin) play important roles in the regulation of sleep/wake. Here we analyze the
in vivo
and
in vitro
phenotype of mice lacking the

GABA
B1

gene specifically in orexin neurons (oxGKO mice) and demonstrate that GABA
B
receptors on orexin neurons are essential in stabilizing and consolidating sleep/wake states. In oxGKO brain slices, we show that the absence of GABA
B
receptors decreases the sensitivity of orexin neurons to both excitatory and inhibitory inputs because of augmented GABA
A
-mediated inhibition that increases the membrane conductance and shunts postsynaptic currents in these neurons. This increase in GABA
A
-mediated inhibitory tone is apparently the result of an orexin receptor type 1-mediated activation of local GABAergic interneurons that project back onto orexin neurons. oxGKO mice exhibit severe fragmentation of sleep/wake states during both the light and dark periods, without showing an abnormality in total sleep time or signs of cataplexy. Thus, GABA
B
receptors on orexin neurons are crucial in the appropriate control of the orexinergic tone through sleep/wake states, thereby stabilizing the state switching mechanisms.
Host cell-free growth of the Q fever bacterium
Coxiella burnetii
Authors: Omsland Anders , Cockrell Diane C. , Howe Dale , Fischer Elizabeth R. , Virtaneva Kimmo , Sturdevant Daniel E. , Porcella Stephen F. , Heinzen Robert A.
Published: February 2009

The inability to propagate obligate intracellular pathogens under axenic (host cell-free) culture conditions imposes severe experimental constraints that have negatively impacted progress in understanding pathogen virulence and disease mechanisms.
Coxiella burnetii
, the causative agent of human Q (Query) fever, is an obligate intracellular bacterial pathogen that replicates exclusively in an acidified, lysosome-like vacuole. To define conditions that support
C. burnetii
growth, we systematically evaluated the organism's metabolic requirements using expression microarrays, genomic reconstruction, and metabolite typing. This led to development of a complex nutrient medium that supported substantial growth (approximately 3 log
10
) of
C. burnetii
in a 2.5% oxygen environment. Importantly, axenically grown
C. burnetii
were highly infectious for Vero cells and exhibited developmental forms characteristic of in vivo grown organisms. Axenic cultivation of
C. burnetii
will facilitate studies of the organism's pathogenesis and genetics and aid development of Q fever preventatives such as an effective subunit vaccine. Furthermore, the systematic approach used here may be broadly applicable to development of axenic media that support growth of other medically important obligate intracellular pathogens.
A retrograde signal from RyR1 alters DHP receptor inactivation and limits window Ca
2+
release in muscle fibers of Y522S RyR1 knock-in mice
Authors: Andronache Zoita , Hamilton Susan L. , Dirksen Robert T. , Melzer Werner
Published: February 2009

Malignant hyperthermia (MH) is a life-threatening hypermetabolic condition caused by dysfunctional Ca
2+
homeostasis in skeletal muscle, which primarily originates from genetic alterations in the Ca
2+
release channel (ryanodine receptor, RyR1) of the sarcoplasmic reticulum (SR). Owing to its physical interaction with the dihydropyridine receptor (DHPR), RyR1 is controlled by the electrical potential across the transverse tubular (TT) membrane. The DHPR exhibits both voltage-dependent activation and inactivation. Here we determined the impact of an MH mutation in RyR1 (Y522S) on these processes in adult muscle fibers isolated from heterozygous RyR1
Y522S
-knock-in mice. The voltage dependence of DHPR-triggered Ca
2+
release flux was left-shifted by ≈8 mV. As a consequence, the voltage window for steady-state Ca
2+
release extended to more negative holding potentials in muscle fibers of the RyR1
Y522S
-mice. A rise in temperature from 20° to 30 °C caused a further shift to more negative potentials of this window (by ≈20 mV). The activation of the DHPR-mediated Ca
2+
current was minimally changed by the mutation. However, surprisingly, the voltage dependence of steady-state inactivation of DHPR-mediated calcium conductance and release were also shifted by ≈10 mV to more negative potentials, indicating a retrograde action of the RyR1 mutation on DHPR inactivation that limits window Ca
2+
release. This effect serves as a compensatory response to the lowered voltage threshold for Ca
2+
release caused by the Y522S mutation and represents a novel mechanism to counteract excessive Ca
2+
leak and store depletion in MH-susceptible muscle.
Intracerebroventricular amyloid-β antibodies reduce cerebral amyloid angiopathy and associated micro-hemorrhages in aged Tg2576 mice
Authors: Thakker Deepak R. , Weatherspoon Marcy R. , Harrison Jonathan , Keene Thomas E. , Lane Deanna S. , Kaemmerer William F. , Stewart Gregory R. , Shafer Lisa L.
Published: February 2009

Although immunization against amyloid-β (Aβ) holds promise as a disease-modifying therapy for Alzheimer disease (AD), it is associated with an undesirable accumulation of amyloid in the cerebrovasculature [i.e., cerebral amyloid angiopathy (CAA)] and a heightened risk of micro-hemorrhages. The central and peripheral mechanisms postulated to modulate amyloid with anti-Aβ immunotherapy remain largely elusive. Here, we compared the effects of prolonged intracerebroventricular (
icv
) versus systemic delivery of anti-Aβ antibodies on the behavioral and pathological changes in an aged Tg2576 mouse model of AD. Prolonged
icv
infusions of anti-Aβ antibodies dose-dependently reduced the parenchymal plaque burden, astrogliosis, and dystrophic neurites at doses 10- to 50-fold lower than used with systemic delivery of the same antibody. Both
icv
and systemic anti-Aβ antibodies reversed the behavioral impairment in contextual fear conditioning. More importantly, unlike systemically delivered anti-Aβ antibodies that aggravated vascular pathology,
icv
-infused antibodies globally reduced CAA and associated micro-hemorrhages. We present data suggesting that the divergent effects of
icv
-delivered anti-Aβ antibodies result from gradually engaging the local (i.e., central) mechanisms for amyloid clearance, distinct from the mechanisms engaged by high doses of anti-Aβ antibodies that circulate in the vasculature following systemic delivery. With robust efficacy in reversing AD-related pathology and an unexpected benefit in reducing CAA and associated micro-hemorrhages,
icv
-targeted passive immunotherapy offers a promising therapeutic approach for the long-term management of AD.
Dendritic cell targeting ofBacillus anthracisprotective antigen expressed byLactobacillus acidophilusprotects mice from lethal challenge
Authors: Mohamadzadeh M. , Duong T. , Sandwick S. J. , Hoover T. , Klaenhammer T. R.
Published: February 2009

Efficient vaccines potentiate antibody avidity and increase T cell longevity, which confer protection against microbial lethal challenge. A vaccine strategy was established by usingLactobacillus acidophilusto deliverBacillus anthracisprotective antigen (PA) via specific dendritic cell-targeting peptides to dendritic cells (DCs), which reside in the periphery and mucosal surfaces, thus directing and regulating acquired immunity. The efficiency of oral delivery ofL. acidophilusexpressing a PA-DCpep fusion was evaluated in mice challenged with lethalB. anthracisSterne. Vaccination withL. acidophilusexpressing PA-DCpep induced robust protective immunity againstB. anthracisSterne compared with mice vaccinated withL. acidophilusexpressing PA-control peptide or an empty vector. Additionally, serum anti-PA titers, neutralizing PA antibodies, and the levels of IgA-expressing cells were all comparable with the historical recombinant PA plus aluminum hydroxide vaccine administered s.c. Collectively, development of this strategy for oral delivery of DC-targeted antigens provides a safe and protective vaccine via a bacterial adjuvant that may potentiate mucosal immune responses against deadly pathogens.
Spectroscopic studies of position-specific DNA “breathing” fluctuations at replication forks and primer-template junctions
Authors: Jose Davis , Datta Kausiki , Johnson Neil P. , von Hippel Peter H.
Published: February 2009

Junctions between ssDNA and dsDNA sequences are important in many cellular processes, including DNA replication, transcription, recombination, and repair. Significant transient conformational fluctuations (“DNA breathing”) can occur at these ssDNA–dsDNA junctions. The involvement of such breathing in the mechanisms of macromolecular complexes that operate at these loci is not well understood, in part because these fluctuations have been difficult to measure in a position-specific manner. To address this issue we constructed forked or primer-template DNA constructs with 1 or 2 adjacent 2-aminopurine (2-AP) nucleotide residues (adenine analogues) placed at specific positions on both sides of the ssDNA–dsDNA junction. Unlike canonical DNA bases, 2-AP absorbs, fluoresces, and displays CD spectra at wavelengths >300 nm, where other nucleic acid and protein components are transparent. We used CD and fluorescence spectra and acrylamide quenching of these probes to monitor the extent and nature of DNA breathing of A-T base pairs at specific positions around the ssDNA–dsDNA junction. As expected, spectroscopically measurable unwinding penetrates ≈2 bp into the duplex region of these junctions under physiological conditions for the constructs examined. Surprisingly, we found that 2-AP bases at ssDNA sites directly adjacent to ssDNA–dsDNA junctions are significantly more unstacked than those at more distant ssDNA positions. These local and transient DNA conformations on both sides of ssDNA–dsDNA junctions may serve as specific interaction targets for enzymes that manipulate DNA in the processes of gene expression.
Fermented liquid feed for pigs.
Authors: Brooks P. H.
Published: February 2009

Liquid feeding systems develop a microflora that usually becomes dominated by lactic acid bacteria (LAB), and this can be beneficial to the health of the pigs. When levels greater than 100 mM lactic acid are generated in liquid feed (LF), this can significantly reduce the numbers of enteropathogens and reduce the incidence of
Salmonella
. Using fermented co-products from the human food industry or deliberately fermenting LF has the potential to improve gut health and nutrient utilization. The evidence indicates that spontaneous fermentation of LF is unreliable and fails to yield consistently good results. Maintaining a continuous fermentation by retaining a proportion of the feed each day can result in the development of a resident microflora dominated by yeasts. This may compromise both palatability and health and reduce the nutritional value of the feed. Batch fermentation of the cereal portion of the diet using inoculants selected to generate high concentrations of lactic acid has the potential to produce more consistent results. This approach may enable the combination of the preservative and probiotic effects of LAB, while also improving the availability of nutrients in the feed and reducing levels of anti-nutrients and mycotoxins. Accurate assessment of these changes will enable nutritionists to modify raw material specifications and constraints to take advantage of these improvements, and in so doing, improve pig performance and reduce environmental impact.
Crop-based biodegradable packaging and its environmental implications.
Authors: Cruz-Romero M. , Kerry J. P.
Published: February 2009

With the sharp rise in global prices for petroleum, growing concerns about the depletion of non-renewable raw materials and the worldwide interest in sustainability, responsible packaging production and an effective management of waste has created a growing interest in developing crop-based packaging materials. Crop-based packaging materials can be biodegradable and/or compostable and may offer a possible alternative to traditional synthetic materials, consequently reducing the environmental impacts relating to packaging material usage. Until recently, crop-based packaging materials had been considered a novelty in the market, with traditional synthetic plastics accounting for the vast majority of sales. However, developments in technology, growing consumer demand for environmentally friendly packaging and improved economics over petrochemical-derived plastics have led to crop-based biodegradable polymers being increasingly seen as highly promising and potential substitutes for petrochemical-derived plastic polymers. Some of the crop-based packaging materials such as polylactide are already competitive alternatives to conventional food packaging, whereas other materials such as starch-based materials will require further optimization in order to be suitable for industrial packaging applications. This review presents an overview of crop-based polymer packaging materials, their potential for industrial usage and their environmental implications. Conclusively, life-cycle analysis studies and environmental assessment data presented as part of this review support the further development of crop-based biodegradable packaging materials, provided that certain ethical issues pertaining to global food price increases, and indeed global food shortages, are considered.
Using transcriptomics to understand the wheat genome.
Authors: Coram T. E. , Brown-Guedira G. , Chen X. M.
Published: February 2009

Wheat (
Triticum aestivum
L.) is one of the most important food crops in the world, and transcriptomics studies of this crop promise to reveal the expression dynamics of genes that control many agriculturally important traits. In this review of wheat transcriptomics research, the current status of transcriptome surveying technology is presented, with particular emphasis on breakthrough techniques that will promote rapid progress in understanding the wheat genome. Microarrays have now become routine in wheat research, and the 55K Affymetrix Wheat GeneChip has enabled the generation of numerous high-quality datasets. In fact, the broad range of gene expression datasets provides future opportunities for integrating these data in a systematic approach that may reveal gene coexpression networks that underlie important traits. Wheat microarrays have also recently been used in other valuable approaches, including simultaneous transcriptome and genome profiling through single-feature polymorphism markers, the mapping of translocation breakpoints, and surveying of antisense transcription. The future use of wheat microarrays for gene expression measurement may be challenged by new sequencing-based transcriptomics techniques. These new techniques are presented, and the application of sequencing-by-synthesis as a future area of wheat transcriptomics research is highlighted. However, the yet to be fully sequenced polyploid wheat genome poses problems for some of these technologies when attempting to annotate and assign short-sequence tags. For this reason, the Roche 454 technology is considered the best option for future progress because of its longer sequence reads that can be more easily annotated, as well as its unbiased potential for covering the entire wheat transcriptome.
Impacts and lessons from BSE episodes.
Authors: Roy D. G. le , Klein K. K.
Published: February 2009

This review provides an overview of consumer and government responses to bovine serum encephalopathy (BSE) and draws lessons for industry stakeholders. The approaches taken around the world to contain the risk of BSE where it was discovered reveal important patterns, differences and difficulties. Important lessons are drawn in three areas: (1) the paramount position of consumers of beef with respect to production, processing and regulatory activities; (2) the importance of clearly communicating relative risks of infection to the public; and (3) the critical role of improved international trade rules to mitigate financial impacts of animal disease outbreaks.
Legal, policy and institutional aspects of urban and peri-urban forestry and greening: the case of West and Central Asia.
Authors: Knuth L. , Randrup T. B. , Gauthier M.
Published: February 2009

Owing to increased global urbanization, Food and Agriculture Organization of the United Nations (FAO) initiated a study on the relationship between the urban green resource, with a primary focus on urban and peri-urban forests and greening (UPFG), and urban livelihood and poverty alleviation in West and Central Asia (WECA). The present study is based primarily on a comprehensive review of scientific literature and legal, policy and institutional documents found via the Internet. Policies at national and sub-national levels related to UPFG focus mainly on environmental aspects. The present study found no policies promoting UPFG as a source of income for the livelihood of the urban and peri-urban poor. However, UPFG in the context of poverty alleviation might be addressed by related policies, such as forestry policies. Further, this study found that no particular national or international law governs UPFG; however, most countries of the WECA region are parties to the international conventions related to UPFG. It is concluded that UPFG is not comprehensively addressed at a country level but various laws exist that address UPFG in a fragmentary way. This may be because of the lack of awareness of UPFG as a multisectoral, multifaceted discipline. It is important to pursue the objective to turn degraded elements of urban green resources into environments that can be put to productive use by poor families, thereby offering them income opportunities and/or food for household use. Decentralization is becoming increasingly important in the WECA region. In this context, responsibilities related to UPFG tend to shift to lower government levels. The effect of decentralization policies will also lead to greater involvement of local community groups, municipalities and grass-root organizations in the various aspects of UPFG development and management. However, this requires capacity building and awareness-raising campaigns and sufficient financial resources.
A review of synbiotic supplements on faecal immunoglobulin A in bovine neonates.
Authors: Terrill S. J. , Heinrichs A. J. , Long M. R.
Published: February 2009

Antibiotics have been used with excellent results for over 50 years in livestock industries. The numerous benefits associated with antibiotic treatment have led to widespread subtherapeutic use in raising dairy calves. In recent years, interest in antibiotic alternatives has grown as concerns about antibiotic resistance in animals and humans have been publicized. One alternative is supplementation of calf diets with prebiotics, probiotics or some combination of the two (known as synbiotics). The major benefit of treatment with these products is increased proliferation and growth of healthy gut bacteria. The presence of a healthy intestinal microflora has been shown to benefit the whole body, including increased weight gain, decreased presence of pathogens and enhanced immune function. Although limited research has been done in calves, work with other species has shown that addition of these products to an animal's diet can improve mucosal immune system function, increasing levels of immunoglobulin A (IgA), both in the serum and intestinal mucosa. As the antibody secreted by mucosal surfaces, IgA is considered the first line of defence against infections entering the body. Multiple explanations exist for the mechanism of how probiotic bacteria (and, in turn, prebiotic supplements) increase IgA secretion. It has been proposed that bacterial cell components such as peptidoglycan, cytoplasmic contents and techoic acids may elicit this immune reaction. As more research focuses on mechanisms, and not simply results, of pre-, pro- and synbiotic supplementation, products will be able to be fine-tuned to enhance their function and improve results when fed to calves.
Does the index of segregation matter? The composition of secondary schools in England since 1996
Authors: Gorard Stephen
Published: February 2009

This paper presents a new analysis of segregation between schools in terms of pupils living in poverty, for all secondary schools in England from 1996 to 2005. This shows that the clustering of similar pupils in specific schools increased noticeably from 1996 to 2001, but then settled at a level still below that of 1989 when official records began. The analysis uses four estimates of segregation using figures for take‐up of, and eligibility for, free school meals compiled to create both the dissimilarity index and what has been termed the Gorard index of segregation. All four estimates give the same substantive results and the findings for the dissimilarity index and the Gorard index of segregation using either measure of free school meals are indistinguishable. The two indices are, therefore, measuring the same thing. However, the Gorard index of segregation is again shown to be more tolerant of the precise measure being used and so more strongly composition invariant than the dissimilarity index. This has important implications both for the past debate on how to measure segregation between schools and for how education authorities go about estimating segregation in the future.
Characteristics of integrated 18F-FDG PET/CT in pulmonary cryptococcosis
Authors: Huang Chung-Jen , You Dong-Ling , Lee Pei-Ing , Hsu Li-Han , Liu Chia-Chuan , Shih Chih-Shiun , Shih Chiang-Ching , Tseng Hsiu-Chin
Published: February 2009

Background: Pulmonary cryptococcosis is an uncommon cause of pulmonary nodules found by 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) scans. It is rarely reported but may mislead interpretation.

Purpose: To describe the 18F-FDG PET/CT findings of pulmonary cryptococcosis.

Material and Methods: The 18F-FDG PET/CT images of seven patients with pulmonary cryptococcosis were evaluated.

Results: The 18F-FDG PET/CT exams showed single or multiple nodular lesions. The standardized uptake values (SUV) in early images varied significantly for the seven patients (ranging from 2.2 to 11.6). Delayed SUVs showed significant increases in four patients.

Conclusion: Pulmonary cryptococcosis mimics primary or metastatic lung cancer on 18F-FDG PET/CT scan. Tissue confirmation should be considered for any suspicious pulmonary nodules found on 18F-FDG PET/CT scan with an SUV score higher than 2.5, in order to avoid overdiagnosis or overstaging.
Development of a Flexible, Computerized Database to Prioritize, Record, and Report Influenza Vaccination Rates for Healthcare Personnel
Authors: Melia Michael , O'Neill Sarah , Calderon Sherry , Hewitt Sandra , Orlando Kelly , Bithell-Taylor Karen , Affeln Dieter , Conti Carolyn , Wright Sharon B.
Published: February 2009

Objective.

To describe the method used to develop a flexible, computerized database for recording and reporting rates of influenza vaccination among healthcare personnel who were classified by their individual levels (hereafter, “tiers”) of direct patient contact.

Design.

Three-year descriptive summary.

Setting.

Large, academic, tertiary care medical center in the United States.

Participants.

All of the medical center's healthcare personnel.

Methods.

The need to develop a computer-based system to record direct patient care tiers and vaccination data for healthcare personnel was identified. A plan that was to be implemented in stages over several seasons was developed.

Results.

Direct patient care tiers were defined by consensus opinion on the basis of the extent, frequency, and intensity of direct contact with patients. The definitions of these tiers evolved over 3 seasons. Direct patient care classifications were assigned and recorded in a computerized database, and data regarding the receipt of vaccination were tracked by using the same database. Data were extracted to generate reports of individual, departmental, and institutional vaccination rates, both overall and according to direct patient care tiers.

Conclusions.

Development of a computerized database to record direct patient care tiers for individual healthcare workers is a daunting but manageable task. Widespread use of these direct patient care definitions will facilitate uniform comparisons of vaccination rates between institutions. This computerized database can easily be used by infection control personnel to accomplish several other key tasks, including vaccination triage in the context of shortage or delay, prioritization of personnel to receive interventions in times of crisis, and monitoring the status of other employee health or occupational health measures.