bluuebunny/crossref_metadata_2025 huggingface dataset:
Seasonal cycles of Stratospheric Aerosol and Gas Experiment II near‐background aerosol in the lower stratosphere
Authors: Niwano Masanori , Hayashida Sachiko , Akiyoshi Hideharu , Takahashi Masaaki
Published: July 2009

Extinction data from the Stratospheric Aerosol and Gas Experiment (SAGE) II in the lower stratosphere were analyzed for seasonal cycles in the near‐background levels of stratospheric aerosol. The data analyzed were the extinction coefficient at 0.525 μm (β0.525) and the extinction ratio at 0.525 μm (E0.525) on the basis of climatological zonal monthly mean for the years 1998–2004. Distinct seasonal cycles were found for β0.525 at 35–15°S above 28 km (region A) and at 20°S–30°N from 16 to 20.5 km (region B). In the A region, the seasonal cycle of E0.525 was characterized by a maximum in local fall and can be explained by the ascent of mean meridional circulation in local summer and descent in local winter. In the B region, the seasonal cycles of E0.525 were characterized by a maximum in October‐January, which can be interpreted by meridional transport and mixing. The amplitude of the seasonal cycles for E0.525 exhibited asymmetry between the Northern Hemisphere (NH) and the Southern Hemisphere (SH); the amplitudes at latitudes of 20–30° were larger in the SH than in the NH above 29 km, whereas they were larger in the NH than in the SH below 18 km. Comparison of the distribution of E0.525 with that of SAGE II water vapor suggested that the E0.525 distribution is controlled by the stratospheric circulation and troposphere‐originated gases. One difference between E0.525 and water vapor was found in the E0.525 maximum that appears over the winter subtropics. The E0.525 maximum can be attributed to the dominance of temperature and microphysical effects compared to transport effects, whereas the water vapor distribution can be attributed to transport effects. Another difference is that an upward propagation of the seasonal cycle of E0.525 at 5°S–30°N disappeared near 23 km. This difference is explained by the fact that the chemical and microphysical processes of aerosol formation become significant above 23 km.
Characteristics of aerosol size distributions and new particle formation in the summer in Beijing
Authors: Yue Dingli , Hu Min , Wu Zhijun , Wang Zhibin , Guo Song , Wehner Birgit , Nowak Andreas , Achtert Peggy , Wiedensohler Alfred , Jung Jinsang , Kim Young J. , Liu Shawchen
Published: July 2009

The Campaigns of Air Quality Research in Beijing and Surrounding Region 2006 (CAREBeijing‐2006) were mainly focused on the influence of the regional aerosol on the air pollution in Beijing. The urban aerosol was characterized in detail. The particle size distributions were also compared to those measured at a regional site (Yufa) approximately 50 km south of the urban site at Peking University (PKU). At PKU, total particle number and volume concentrations were (1.8 ± 0.8) × 104 cm−3 and 83.5 ± 57.9 μm3 cm−3, respectively. Days in three consecutive summers of 2004, 2005, and 2006 were classified as polluted days with PM10 over 150 μg m−3 and nonpolluted days with lower PM10. On nonpolluted days, particle number size distributions showed a maximum at about 60 nm with Aitken mode particles dominating number concentration. On polluted days, the contribution of accumulation mode particles increased, shifting the maximum of the number size distribution to over 80 nm. On polluted days with stagnant meteorological conditions, secondary aerosol dominated, with SO42−, NO3−, and NH4+ accounting for over 60% of accumulation mode particle mass. Particle number size distributions at both sites were similar. Number and volume concentrations of total particles at Yufa were 6% and 12% lower, respectively; those of accumulation mode particles were 2% and 15% lower. This means that air pollution in Beijing is mainly a regional problem. The regional accumulation mode particles are a metric for assessing the air quality since they influence most the visibility and total mass concentration. Their number and volume concentrations on polluted days were 5 × 103 cm−3 and 30 μm3 cm−3, respectively. Five new particle formation (NPF) events with continuous smooth growth were observed at both PKU and Yufa during CAREBeijing‐2006. These NPF events are regional or semiregional. Growth rates at PKU ranged from 1.2 to 5.6 nm h−1, and formation rates ranged from 1.1 to 22.4 cm−3 s−1. SO42−, NH4+, and oxalate might be important contributors to NPF events.
Reduction of systematic errors in regional climate simulations of the summer monsoon over East Asia and the western North Pacific by applying the spectral nudging technique
Authors: Cha Dong‐Hyun , Lee Dong‐Kyou
Published: July 2009

In this study, the systematic errors in regional climate simulation of 28‐year summer monsoon over East Asia and the western North Pacific (WNP) and the impact of the spectral nudging technique (SNT) on the reduction of the systematic errors are investigated. The experiment in which the SNT is not applied (the CLT run) has large systematic errors in seasonal mean climatology such as overestimated precipitation, weakened subtropical high, and enhanced low‐level southwesterly over the subtropical WNP, while in the experiment using the SNT (the SP run) considerably smaller systematic errors are resulted. In the CTL run, the systematic error of simulated precipitation over the ocean increases significantly after mid‐June, since the CTL run cannot reproduce the principal intraseasonal variation of summer monsoon precipitation. The SP run can appropriately capture the spatial distribution as well as temporal variation of the principal empirical orthogonal function mode, and therefore, the systematic error over the ocean does not increase after mid‐June. The systematic error of simulated precipitation over the subtropical WNP in the CTL run results from the unreasonable positive feedback between precipitation and surface latent heat flux induced by the warm sea surface temperature anomaly. Since the SNT plays a role in decreasing the positive feedback by improving monsoon circulations, the SP run can considerably reduce the systematic errors of simulated precipitation as well as atmospheric fields over the subtropical WNP region.
The regulation of protein phosphorylation
Authors: Johnson Louise N.
Published: July 2009

Phosphorylation plays essential roles in nearly every aspect of cell life. Protein kinases regulate signalling pathways and cellular processes that mediate metabolism, transcription, cell-cycle progression, differentiation, cytoskeleton arrangement and cell movement, apoptosis, intercellular communication, and neuronal and immunological functions. Protein kinases share a conserved catalytic domain, which catalyses the transfer of the γ-phosphate of ATP to a serine, threonine or tyrosine residue in protein substrates. The kinase can exist in an active or inactive state regulated by a variety of mechanisms in different kinases that include control by phosphorylation, regulation by additional domains that may target other molecules, binding and regulation by additional subunits, and control by protein–protein association. This Novartis Medal Lecture was delivered at a meeting on protein evolution celebrating the 200th anniversary of Charles Darwin's birth. I begin with a summary of current observations from protein sequences of kinase phylogeny. I then review the structural consequences of protein phosphorylation using our work on glycogen phosphorylase to illustrate one of the more dramatic consequences of phosphorylation. Regulation of protein phosphorylation is frequently disrupted in the diseased state, and protein kinases have become high-profile targets for drug development. Finally, I consider recent advances on protein kinases as drug targets and describe some of our recent work with CDK9 (cyclin-dependent kinase 9)–cyclin T, a regulator of transcription.
Inhibitors of protein aggregation and toxicity
Authors: Amijee Hozefa , Madine Jill , Middleton David A. , Doig Andrew J.
Published: July 2009

The aggregation of numerous peptides or proteins has been linked to the onset of disease, including Aβ (amyloid β-peptide) in AD (Alzheimer's disease), asyn (α-synuclein) in Parkinson's disease and amylin in Type 2 diabetes. Diverse amyloidogenic proteins can often be cut down to an SRE (self-recognition element) of as few as five residues that retains the ability to aggregate. SREs can be used as a starting point for aggregation inhibitors. In particular, N-methylated SREs can bind to a target on one side, but have hydrogen-bonding blocked on their methylated face, interfering with further assembly. We applied this strategy to develop Aβ toxicity inhibitors. Our compounds, and a range of compounds from the literature, were compared under the same conditions, using biophysical and toxicity assays. Two N-methylated D-peptide inhibitors with unnatural side chains were the most effective and can reverse Aβ-induced inhibition of LTP (long-term potentiation) at concentrations as low as 10 nM. An SRE in asyn (VAQKTV) was identified using solid-state NMR. When VAQKTV was N-methylated, it was able to disrupt asyn aggregation. N-methylated derivatives of the SRE of amylin are also able to inhibit amylin aggregation.
Functionalized nanoparticles for bioanalysis by SERRS
Authors: Graham Duncan , Faulds Karen , Thompson David , McKenzie Fiona , Stokes Robert , Dalton Colette , Stevenson Ross , Alexander Jim , Garside Paul , McFarlane Emma
Published: July 2009

Metallic nanoparticles can be used as basic materials for a wide variety of purposes including building blocks for nanoassemblies, substrates for enhanced spectroscopies such as fluorescence and Raman and as labels for biomolecules. In the present paper, we report how silver and gold nanoparticles can be functionalized with specific biomolecular probes to interact in a specific manner with a target molecule to provide a change in the properties of the nanoparticles which can be measured to indicate the molecular recognition event. Examples of this approach include DNA hybridization to switch on SERRS (surface-enhanced resonance Raman scattering) when a specific target sequence is present, the use of nanoparticles for in vivo SERRS imaging and the use of nanoparticles functionalized with antibodies to provide a new type of immunoassay. These examples indicate how nanoparticles can be used to provide highly sensitive and informative data from a variety of biological systems when used in combination with SERRS.
Model-based evolutionary analysis: the natural history of phage-shock stress response
Authors: Huvet Maxime , Toni Tina , Tan Hui , Jovanovic Goran , Engl Christoph , Buck Martin , Stumpf Michael P.H.
Published: July 2009

The evolution of proteins is inseparably linked to their function. Because most biological processes involve a number of different proteins, it may become impossible to study the evolutionary properties of proteins in isolation. In the present article, we show how simple mechanistic models of biological processes can complement conventional comparative analyses of biological traits. We use the specific example of the phage-shock stress response, which has been well characterized in Escherichia coli, to elucidate patterns of gene sharing and sequence conservation across bacterial species.
Angioplasticity in asthma
Authors: Asosingh Kewal , Erzurum Serpil C.
Published: July 2009

Plasticity of the lung vasculature is intrinsically more complex than other organs due to the presence of two blood supply systems under different arterial pressures, the pulmonary and bronchial arterial systems. The bronchial and pulmonary circulations may both contribute to vascular remodelling in lungs after injury or inflammation. Vascular remodelling in the airway is a long recognized component in asthma. Growing numbers of reports suggest that a pro-angiogenic milieu is not a consequence of, but rather dictates the chronic inflammation of asthma. The fairly recent discovery of EPCs (endothelial progenitor cells) has enabled us to study the bone-marrow-derived cells that regulate lung vascular plasticity in asthma. This mini review provides a concise synopsis of our present knowledge about vascular plasticity in adult lungs, summarizes our current view of angioplasticity in asthma and highlights yet unresolved areas of potential interest.
The innate immune rheostat: influence on lung inflammatory disease and secondary bacterial pneumonia
Authors: Hussell Tracy , Cavanagh Mary M.
Published: July 2009

The activity of innate immunity is not simply dictated by the presence of an antigen but also by the balance between negative regulatory and immune potentiator pathways. Even in the absence of antigen, innate immunity can ‘inflame’ if negative regulators are absent. This resting state is adaptable and dictated by environmental influences, host genetics and past infection history. A return to homoeostasis post inflammation may therefore not leave the tissue in an identical state to that prior to the inflammatory event. This adaptability makes us all unique and also explains the variable outcome experienced by a diverse population to the same inflammatory stimulus. Using murine models we have identified that influenza virus causes a long-term modification of the lung microenvironment by a de-sensitization to bacterial products and an increase in the myeloid negative regulator CD200R (CD200 receptor). These two events prevent subsequent inflammatory damage while the lung is healing, but also they may predispose to bacterial colonization of the lower respiratory tract should regulatory mechanisms overshoot. In the extreme, this leads to bacterial pneumonia, sepsis and death. A deeper understanding of the consequences arising from innate immune cell alteration during influenza infection and the subsequent development of bacterial complications has important implications for future drug development.
Twins studies as a model for studies on the interaction between smoking and genetic factors in the development of chronic bronchitis
Authors: Svartengren Magnus , Engström Gunnar , Anderson Martin , Hallberg Jenny , Edula Goutham , Verdier Maria Gerhardsson de , Dahlbäck Magnus , Lindberg Claes M. , Forsman-Semb Kristina , Nihlén Ulf , Fehniger Thomas E.
Published: July 2009

Smoking is the main risk factor for COPD (chronic obstructive pulmonary disease) but genetic factors are of importance, since only a subset of smokers develops the disease. Sex differences have been suggested both in disease prevalence and response to environmental exposures. Furthermore, it has been shown that acquisition of ‘addiction’ to smoking is partly genetically mediated. Disease cases and smoking habits were identified in 44919 twins aged >40 years from the Swedish Twin Registry. Disease was defined as self-reported chronic bronchitis or emphysema, or recurrent cough with phlegm. The results showed that chronic bronchitis seems to be more prevalent among females, and that the heritability estimate for chronic bronchitis was a moderate 40% and only 14% of the genetic influences were shared by smoking. In addition, 392 twins have been invited to a clinical investigation to evaluate: (i) to what extent genetic factors contribute to individual differences (variation) in FEV1 (forced expiratory volume in 1 s), vital capacity and DLCO (diffusion capacity), taking sex into consideration, and (ii) whether smoking behaviour and respiratory symptoms influence these estimates.
Accelerated lung aging: a novel pathogenic mechanism of chronic obstructive pulmonary disease (COPD)
Authors: MacNee William
Published: July 2009

An enhanced or abnormal inflammatory response to the lungs to inhaled particles and gases, usually from cigarette smoke, is considered to be a general pathogenic mechanism in COPD (chronic obstructive pulmonary disease). Activation of leucocytes and the development of oxidant–antioxidant and protease–anti-protease imbalances are thought to be important aspects of this enhanced inflammatory response to cigarette smoke. The mechanisms involved in the perpetuation of the inflammatory response in the lungs in patients who develop COPD, even after smoking cessation, are not fully established and are key to our understanding of the pathogenic mechanisms in COPD and may be important for the development of new therapies. There is a relationship between chronic inflammatory diseases and aging, and the processes involved in aging may provide a novel mechanism in the pathogenesis of COPD. There is good evidence linking aging and COPD. During normal aging, pulmonary function deteriorates progressively and pulmonary inflammation increases, accompanied in the lungs by the features of emphysema. These features are accelerated in COPD. Emphysema is associated with markers of accelerated aging in the lungs, and COPD is also associated with features of accelerated aging in other organs, such as the cardiovascular and musculoskeletal systems. Cigarette smoke and other oxidative stresses result in cellular senescence and accelerate lung aging. There is also evidence that anti-aging molecules such as histone deacetylases and sirtuins are decreased in the lungs of COPD patients, compared with smokers without COPD, resulting in enhanced inflammation and further progression of COPD. The processes involved in accelerated aging may provide novel targets for therapy in COPD. The present article reviews the evidence for accelerated aging as a mechanism in the pathogenesis of COPD.
Role of integrin-mediated TGFβ activation in the pathogenesis of pulmonary fibrosis
Authors: Goodwin Amanda , Jenkins Gisli
Published: July 2009

IPF (idiopathic pulmonary fibrosis) is a chronic progressive disease of unknown aetiology without effective treatment. IPF is characterized by excessive collagen deposition within the lung. Recent evidence suggests that the lung epithelium plays a key role in driving the fibrotic response. The current paradigm suggests that, after epithelial injury, there is impaired epithelial proliferation and enhanced epithelial apoptosis. This in turn promotes lung fibrosis through impaired basement membrane repair and increased epithelial–mesenchymal transition. Furthermore, fibroblasts are recruited to the wounded area and adopt a myofibroblast phenotype, with the up-regulation of matrix-synthesizing genes and down-regulation of matrix-degradation genes. There is compelling evidence that the cytokine TGFβ (transforming growth factor β) plays a central role in this process. In normal lung, TGFβ is maintained in an inactive state that is tightly regulated temporally and spatially. One of the major TGFβ-activation pathways involves integrins, and the role of the αvβ6 integrin has been particularly well described in the pathogenesis of IPF. Owing to the pleiotropic nature of TGFβ, strategies that inhibit activation of TGFβ in a cell- or disease-specific manner are attractive for the treatment of chronic fibrotic lung conditions. Therefore the molecular pathways that lead to integrin-mediated TGFβ activation must be precisely defined to identify and fully exploit novel therapeutic targets that might ultimately improve the prognosis for patients with IPF.
Induced sputum: a window to lung pathology
Authors: Nicholas Ben , Djukanović Ratko
Published: July 2009

Sputum is recognized as a sampling method for the monitoring and assessment of chronic lung diseases such as asthma, COPD (chronic obstructive pulmonary disease) and cystic fibrosis. Sputum samples the central airways and its protein components (e.g. mucins and cytokines), cellular components (e.g. eosinophils and neutrophils) and microbiological components (e.g. viruses and bacteria) can be used as markers of disease severity, exacerbation, susceptibility or progression. This paper describes the basic constituents of induced sputum and how these influence the quantification and identification of novel biomarkers of chronic lung diseases using techniques such as proteomics.
Regulation of mucin expression in respiratory diseases
Authors: Turner Jonathan , Jones Carol E.
Published: July 2009

Respiratory diseases such as asthma and COPD (chronic obstructive pulmonary disease) are characterized by increased numbers of goblet cells and excessive mucus production, which contribute to the underlying disease pathology. Mucins form a major component of the mucus contributing to its viscoelastic properties, and in the airways the mucins MUC5AC and MUC5B are found at increased levels in both asthmatic and COPD subjects. A diverse range of stimuli have been shown to regulate MUC5AC expression and cause increases in the number of mucus-producing goblet cells. Perhaps the best characterized of these mediators is the cytokine IL (interleukin)-13, which causes increases in MUC5AC-expressing goblet cells in the airways. Several transcription factors have been linked with goblet cell formation and mucus production and include STAT6 (signal transducer and activator of transcription 6), FOXA2 (forkhead box A2) and the SPDEF [SAM (sterile α motif) domain-containing prostate-derived Ets factor]. In mouse airways, goblet cells are normally rare or absent, but increase rapidly in number in response to certain stimuli. The origins of these goblet cells are not well understood, although Clara cells and ciliated cells have been implicated as goblet cell progenitors. An understanding of the origin and processes regulating goblet cell formation in human airway epithelial cells has important implications for the identification of therapeutic targets to treat respiratory diseases.
Inhibition of inducible nitric oxide synthase in respiratory diseases
Authors: Hesslinger Christian , Strub Andreas , Boer Rainer , Ulrich Wolf-Rüdiger , Lehner Martin D. , Braun Clemens
Published: July 2009

Nitric oxide (NO) is a key physiological mediator and disturbed regulation of NO release is associated with the pathophysiology of almost all inflammatory diseases. A multitude of inhibitors of NOSs (nitric oxide synthases) have been developed, initially with low or even no selectivity against the constitutively expressed NOS isoforms, eNOS (endothelial NOS) and nNOS (neuronal NOS). In the meanwhile these efforts yielded potent and highly selective iNOS (inducible NOS) inhibitors. Moreover, iNOS inhibitors have been shown to exert beneficial anti-inflammatory effects in a wide variety of acute and chronic animal models of inflammation. In the present mini-review, we summarize some of our current knowledge of inhibitors of the iNOS isoenzyme, their biochemical properties and efficacy in animal models of pulmonary diseases and in human disease itself. Moreover, the potential benefit of iNOS inhibition in animal models of COPD (chronic obstructive pulmonary disease), such as cigarette smoke-induced pulmonary inflammation, has not been explicitly studied so far. In this context, we demonstrated recently that both a semi-selective iNOS inhibitor {L-NIL [N6-(1-iminoethyl)-L-lysine hydrochloride]} and highly selective iNOS inhibitors (GW274150 and BYK402750) potently diminished inflammation in a cigarette smoke mouse model mimicking certain aspects of human COPD. Therefore, despite the disappointing results from recent asthma trials, iNOS inhibition could still be of therapeutic utility in COPD, a concept which needs to be challenged and validated in human disease.
Modelling the comet assay
Authors: McArt Darragh G. , McKerr George , Howard C. Vyvyan , Saetzler Kurt , Wasson Gillian R.
Published: July 2009

The single-cell gel electrophoresis technique or comet assay is widely regarded as a quick and reliable method of analysing DNA damage in individual cells. It has a proven track record from the fields of biomonitoring to nutritional studies. The assay operates by subjecting cells that are fixed in agarose to high salt and detergent lysis, thus removing all the cellular content except the DNA. By relaxing the DNA in an alkaline buffer, strands containing breaks are released from supercoiling. Upon electrophoresis, these strands are pulled out into the agarose, forming a tail which, when stained with a fluorescent dye, can be analysed by fluorescence microscopy. The intensity of this tail reflects the amount of DNA damage sustained. Despite being such an established and widely used assay, there are still many aspects of the comet assay which are not fully understood. The present review looks at how the comet assay is being used, and highlights some of its limitations. The protocol itself varies among laboratories, so results from similar studies may vary. Given such discrepancies, it would be attractive to break the assay into components to generate a mathematical model to investigate specific parameters.
A simplified approach to estimating total trap contributions in negative bias temperature instability
Authors: Devine R. A. B. , Mee J. K. , Hjalmarson H. P. , Quevedo-Lopez M. A. , Alshareef H. N.
Published: July 2009

A simplified approach is used to determine the relative importance of slow (>3 s) and fast (<3 s) charged trap contributions to threshold voltage shifts (ΔVth) induced by negative bias temperature instability in HfSiON gate dielectric p-channel field effect transistors. For the devices under study the relative importance of the two components is approximately the same. Total trap density induced threshold voltage shifts from measurements at 368, 398, and 428 K can be fitted to a simplified law of the form ΔVth=Ae−EA/kTtα with EA=0.085±0.012 eV and α=0.186±0.003. The importance of ignoring fast trap effects in overestimating reliability lifetimes is discussed.
Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study
Authors: Kneller Gerald R. , Hinsen Konrad
Published: July 2009

We propose a simple analytical model for the elastic incoherent structure factor of proteins measured by neutron scattering, which allows extracting the distribution of atomic position fluctuations from a fit of the model to the experimental data. The method is validated by applying it to elastic incoherent structure factors of lysozyme which have been obtained by molecular dynamics simulation and by normal mode analysis, respectively, and for which distributions of the atomic position fluctuations can be generated numerically for direct comparison with the predictions of the model. The comparison shows a remarkable agreement, in particular, concerning the lower limit for the position fluctuations, which is pronounced in the numerical data.
Hysteresis loops of an assembly of superparamagnetic nanoparticles with uniaxial anisotropy
Authors: Usov N. A. , Grebenshchikov Yu. B.
Published: July 2009

A simple kinetic approach based on approximate solution of the Fokker–Planck equation for magnetic moment orientations is developed for the calculation of the hysteresis loop of a superparamagnetic nanoparticle assembly with predominantly uniaxial magnetic anisotropy. The hysteresis loops of the oriented assembly have been obtained in the intermediate to high damping limit as a function of temperature at various angles that the applied magnetic field makes with the particle easy anisotropy axis. An analytic approximation is given for the effective energy barriers separating energy wells. The evolution of the hysteresis loop as a function of temperature is shown to take place between the ultimate Stoner–Wohlfarth loop and the equilibrium magnetization curve. Analytical estimates for the coercive force and the blocking temperature are obtained both for ordered and randomly oriented assemblies of uniaxial particles.
Application of nanoparticle-containing laser plasmas for optical harmonic generation
Authors: Ganeev R. A. , Bom L. B. Elouga , Ozaki T.
Published: July 2009

Nanoparticle-containing media can be used for efficient high-order harmonic generation of laser radiation. We present the results of studies of the harmonics generated in the laser-produced plasmas containing Cr2O3, Ag, Cu, and Au nanoparticles. These results are compared with the harmonics generated in the plasma produced on the surface of bulk targets at different delays between the subnanosecond heating prepulse and femtosecond pulse and different intensities of prepulse on the target surface. We discuss the harmonic enhancement, which was observed in the case of nanoparticle-containing plumes with regard to the monoparticle-containing plasmas. Morphological studies of plasma debris confirmed the presence and integrity of nanoparticles in the plumes.
Improving the lifetime of white polymeric organic light-emitting diodes
Authors: Gather Malte C. , Köber Sebastian , Heun Susanne , Meerholz Klaus
Published: July 2009

We report on efficient polymeric white organic light-emitting diodes with unprecedented stability. The investigated devices are based on an electroluminescent copolymer of electron and hole-transporting units and red-, green-, and blue-emitting chromophores. We find that the glass transition of the polymer (Tg=182.5 °C) is the process determining the relation between thermal annealing during fabrication and device lifetime. For devices annealed below Tg, the device lifetime significantly increases with increasing annealing temperature. For annealing temperatures above Tg, however, the current density in the devices rapidly increases while their lifetime slightly decreases. Insight into the underlying processes is provided by atomic force microscopy phase imaging and by UV/visible and fluorescence spectroscopy. We also investigated the influence of the operating temperature of the device: besides the commonly known fact that elevated operating temperatures reduce the lifetime, we discovered that the acceleration coefficient, which determines the scaling of the device lifetime with applied current density, was reduced. At the glass transition, the device lifetime no longer depended on the current density. The device lifetime was improved even further by introducing an additional cross-linkable hole-transport layer. Optimized devices achieve a half-luminance lifetime of 1860 h when operated at room temperature and at an initial luminance of 500 cd m−2. As a result of the relatively balanced stability of the three chromophores, the emission spectrum remains virtually unchanged over the entire device lifetime. Finally, to reduce the time required for the lifetime measurements, we propose to analyze the voltage increase over the first 10–50 h of the lifetime test and find that this allows precisely estimating the lifetime of our devices.
Investigation of (110) SnO2 growth mechanisms on TiO2 substrates by plasma-assisted molecular beam epitaxy
Authors: Tsai M. Y. , White M. E. , Speck J. S.
Published: July 2009

We investigated the growth mechanisms of (110) SnO2 on (110) TiO2 by varying tin fluxes under a fixed oxygen pressure by plasma-assisted molecular beam epitaxy. A growth diagram was constructed that consists of two distinct growth regimes: an increase in growth rates in an oxygen-rich environment and a decrease in growth rates in a tin-rich environment. The excess tin played an important role for the unexpected decreasing growth rate in a tin-rich regime. Without a buildup of the tin adlayer coverage, the accumulation of macroscopic tin droplets on the SnO2 film surface was confirmed by the spotty high energy electron diffraction pattern and the absence of intensity oscillations. No SnO2 growth was observed when the impinging tin flux was larger than twice the stoichiometric tin flux, suggesting that all active oxygen atoms were consumed by evaporated tin atoms to form volatile tin suboxide (SnO). The formation of volatile SnO, causing the decreasing growth rate in a tin-rich condition, was monitored by in situ quadrupole mass spectrometry.
Birefringence and absorption coefficients of alpha barium borate in terahertz range
Authors: Liu Jingle , Zhang X. C.
Published: July 2009

In this paper we experimentally investigated the birefringence and absorption coefficients of alpha barium borate (α-BBO) crystal in the range of 0.3–10 THz by using a broadband air photonic terahertz time-domain spectrometer in both transmission and reflection modes. Several phonon modes were observed for o and e beams. The highest phonon mode at 6.8 THz has absorption coefficient of 1000 cm−1. The comparison between the optical properties of the α-BBO and beta barium borate crystals showed that their phonon frequencies are different and α-BBO crystal has smaller refractive index, birefringence, and absorption coefficients in low frequency region. The blueshift behavior of the lowest phonon of the α-BBO crystal over the temperature range of 10–293 K has also been characterized.
Threading dislocation evolution in patterned GaN nanocolumn growth and coalescence overgrowth
Authors: Chen Yung-Sheng , Shiao Wen-Yu , Tang Tsung-Yi , Chang Wen-Ming , Liao Che-Hao , Lin Cheng-Hung , Shen Kun-Ching , Yang C. C. , Hsu Ming-Chi , Yeh Jui-Hung , Hsu Ta-Cheng
Published: July 2009

Threading dislocation (TD) evolution during patterned GaN nanocolumn (NC) growth and coalescence overgrowth with metal-organic chemical vapor deposition is studied based on the comparisons of NC and coalescence overgrowth samples of different NC cross-section diameters and spacing sizes. From the measurement results of depth-dependent x-ray diffraction and cross-section transmission electron microscopy, it is found that the TD density in an NC depends on the patterned hole size for NC growth. Also, the TD formation at the beginning of coalescence overgrowth is related to the NC spacing size. Although the TD density at the bottom of the overgrown layer is weakly dependent on NC and spacing sizes, at its top surface, the TD density strongly relies on NC size. Among the overgrowth samples of different NC diameters and spacing sizes with a fixed NC diameter/spacing ratio, the one with the smallest size and spacing leads to the lowest TD density, the largest lateral domain size, and the highest photoluminescence efficiency. Also, the optical and crystal qualities at the surfaces of all the overgrowth samples are superior to those of a GaN template.
Discrete Wigner function by symmetric informationally complete positive operator valued measure
Authors: Bar-on T.
Published: July 2009

We construct a version of the discrete Wigner function making use of symmetric informationally complete positive operator valued measure. We will show that this version is the natural discrete analog of continuous Wigner function. In addition, to this discrete Wigner function has many properties of the continuous Wigner function.
Rheology of hyperbranched polymer melts undergoing planar Couette flow
Authors: Le T. C. , Todd B. D. , Daivis P. J. , Uhlherr A.
Published: July 2009

The melt rheology of four hyperbranched polymer structures with different molecular weights has been studied using nonequilibrium molecular dynamics (NEMD). Systems were simulated over a wide range of strain rates to capture the crossover behavior from Newtonian to non-Newtonian regimes. Rheological properties including shear viscosity and first and second normal stress coefficients were computed and the transition to shear thinning was observed at different strain rates for hyperbranched polymers of different sizes. The results were consistent with previous findings from NEMD simulation of linear and dendritic polymers. Flow birefringence was characterized by taking into account both form and intrinsic birefringences, which result from molecular and bond alignment, respectively. The stress optical rule was tested and shown to be valid only in the Newtonian regime and violated in the strong flow regime where the rule does not take into account flow-induced changes of the microstructure.
Surface selective binding of nanoclay particles to polyampholyte protein chains
Authors: Pawar Nisha , Bohidar H. B.
Published: July 2009

Binding of nanoclay (Laponite) to gelatin-A and gelatin-B (both polyampholytes) molecules was investigated at room temperature (25 °C) both experimentally and theoretically. The stoichiometric binding ratio between gelatin and Laponite was found to be strongly dependent on the solution ionic strength. Large soluble complexes were formed at higher ionic strengths of the solution, a result supported by data obtained from light scattering, viscosity, and zeta potential measurements. The binding problem was theoretically modeled by choosing a suitable two-body screened Coulomb potential, U(R+)=(q−/2ε)[(Q−/R−)e−kR−−(Q+/R+)e−kR+], where the protein dipole has charges Q+ and Q_ that are located at distances R+ and R_ from the point Laponite charge q− and the dispersion liquid has dielectric constant (ε). U(R+) accounted for electrostatic interactions between a dipole (protein molecule) and an effective charge (Laponite particle) located at an angular position θ. Gelatin-A and Laponite association was facilitated by a strong attractive interaction potential that led to preferential binding of the biopolymer chains to negatively charged face of Laponite particles. In the case of gelatin-B selective surf ace patch binding dominated the process where the positively charged rim and negatively charged face of the particles were selectively bound to the oppositely charged segments of the biopolymer. The equilibrium separation (Re) between the protein and nanoclay particle revealed monovalent salt concentration dependence given by Re∼[NaCl]α where α=0.6±0.2 for gelatin-A and α=0.4±0.2 for gelatin-B systems. The equilibrium separations were ≈30% less compared to the gelatin-A system implying preferential short-range ordering of the gelatin-B–nanoclay pair in the solvent.
Can short-range hybrids describe long-range-dependent properties?
Authors: Henderson Thomas M. , Izmaylov Artur F. , Scalmani Giovanni , Scuseria Gustavo E.
Published: July 2009

Long-range-corrected hybrids, which incorporate all of the long-range exact exchange interaction, improve performance for a host of molecular properties. The long-range portion of exact exchange is both computationally and formally problematic in solids, and screened hybrids therefore eliminate it. While screened hybrids give similar results to their parent global hybrids for many molecular properties, one may worry that they perform poorly for those properties that are improved by the long-range-correction procedure. In this paper, we show that at least for the Heyd–Scuseria–Ernzerhof (HSE) screened hybrid, this is not the case; for many properties improved by long-range-correction, screened hybrids and global hybrids deliver essentially the same results. We suggest that this is because screened hybrids and global hybrids have fundamentally the same many-electron self-interaction error. We also introduce some small revisions to our computational implementation of the HSE screened hybrid, and we recommend these revisions for future applications of HSE.
Efficient evaluation of accuracy of molecular quantum dynamics using dephasing representation
Authors: Li Baiqing , Mollica Cesare , Vaníček Jiří
Published: July 2009

Ab initio methods for the electronic structure of molecules have reached a satisfactory accuracy for calculations of static properties but remain too expensive for quantum dynamics calculations. We propose an efficient semiclassical method for evaluating the accuracy of a lower level quantum dynamics, as compared to a higher level quantum dynamics, without having to perform any quantum dynamics. The method is based on the dephasing representation of quantum fidelity and its feasibility is demonstrated on the photodissociation dynamics of CO2. Our accuracy test can be easily implemented in existing molecular dynamics codes, thus offering wide applicability.
Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure
Authors: Coleman Heather D. , Yan Jimmy , Mansfield Shawn D.
Published: July 2009

Overexpression of the
Gossypium hirsutum
sucrose synthase (
SuSy
) gene under the control of 2 promoters was examined in hybrid poplar (
Populus alba
×
grandidentata
). Analysis of RNA transcript abundance, enzyme activity, cell wall composition, and soluble carbohydrates revealed significant changes in the transgenic lines. All lines showed significantly increased SuSy enzyme activity in developing xylem. This activity manifested in altered secondary cell wall cellulose content per dry weight in all lines, with increases of 2% to 6% over control levels, without influencing plant growth. The elevated concentration of cellulose was associated with an increase in cell wall crystallinity but did not alter secondary wall microfibril angle. This finding suggests that the observed increase in crystallinity is a function of altered carbon partitioning to cellulose biosynthesis rather than the result of tension wood formation. Furthermore, the augmented deposition of cellulose in the transgenic lines resulted in thicker xylem secondary cell wall and consequently improved wood density. These findings clearly implicate SuSy as a key regulator of sink strength in poplar trees and demonstrate the tight association of SuSy with cellulose synthesis and secondary wall formation.
Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome
Authors: Adelson David L. , Raison Joy M. , Edgar Robert C.
Published: July 2009

Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.
Scaling properties of European research units
Authors: Jamtveit Bjørn , Jettestuen Espen , Mathiesen Joachim
Published: July 2009

A quantitative characterization of the scale-dependent features of research units may provide important insight into how such units are organized and how they grow. The relative importance of top-down versus bottom-up controls on their growth may be revealed by their scaling properties. Here we show that the number of support staff in Scandinavian research units, ranging in size from 20 to 7,800 staff members, is related to the number of academic staff by a power law. The scaling exponent of ≈1.30 is broadly consistent with a simple hierarchical model of the university organization. Similar scaling behavior between small and large research units with a wide range of ambitions and strategies argues against top-down control of the growth. Top-down effects, and externally imposed effects from changing political environments, can be observed as fluctuations around the main trend. The observed scaling law implies that cost-benefit arguments for merging research institutions into larger and larger units may have limited validity unless the productivity per academic staff and/or the quality of the products are considerably higher in larger institutions. Despite the hierarchical structure of most large-scale research units in Europe, the network structures represented by the
academic
component of such units are strongly antihierarchical and suboptimal for efficient communication within individual units.
Acetate produced in the mitochondrion is the essential precursor for lipid biosynthesis in procyclic trypanosomes
Authors: Rivière Loïc , Moreau Patrick , Allmann Stefan , Hahn Matthias , Biran Marc , Plazolles Nicolas , Franconi Jean-Michel , Boshart Michael , Bringaud Frédéric
Published: July 2009

Acetyl-CoA produced in mitochondria from carbohydrate or amino acid catabolism needs to reach the cytosol to initiate de novo synthesis of fatty acids. All eukaryotes analyzed so far use a citrate/malate shuttle to transfer acetyl group equivalents from the mitochondrial matrix to the cytosol. Here we investigate how this acetyl group transfer occurs in the procyclic life cycle stage of
Trypanosoma brucei
, a protozoan parasite responsible of human sleeping sickness and economically important livestock diseases. Deletion of the potential citrate lyase gene, a critical cytosolic enzyme of the citrate/malate shuttle, has no effect on de novo biosynthesis of fatty acids from
14
C-labeled glucose, indicating that another route is used for acetyl group transfer. Because acetate is produced from acetyl-CoA in the mitochondrion of this parasite, we considered genes encoding cytosolic enzymes producing acetyl-CoA from acetate. We identified an acetyl-CoA synthetase gene encoding a cytosolic enzyme (AceCS), which is essential for cell viability. Repression of AceCS by inducible RNAi results in a 20-fold reduction of
14
C-incorporation from radiolabeled glucose or acetate into de novo synthesized fatty acids. Thus, we demonstrate that the essential cytosolic enzyme AceCS of
T. brucei
is responsible for activation of acetate into acetyl-CoA to feed de novo biosynthesis of lipids. To date,
Trypanosoma
is the only known eukaryotic organism that uses acetate instead of citrate to transfer acetyl groups over the mitochondrial membrane for cytosolic lipid synthesis.
Role of human noncoding RNAs in the control of tumorigenesis
Authors: Li Ling , Feng Tingting , Lian Yingying , Zhang Guangfeng , Garen Alan , Song Xu
Published: July 2009

Related studies showed that the protein PSF represses proto-oncogene transcription, and VL30–1 RNA, a mouse noncoding retroelement RNA, binds and releases PSF from a proto-oncogene, activating transcription. Here we show that this mechanism regulates tumorigenesis in human cells, with human RNAs replacing VL30–1 RNA. A library of human RNA fragments was used to isolate, by affinity chromatography, 5 noncoding RNA fragments that bind to human PSF (hPSF), releasing hPSF from a proto-oncogene and activating transcription. Each of the 5 RNA fragments maps to a different human gene. The tumorigenic function of the hPSF-binding RNAs was tested in a human melanoma line and mouse fibroblast line, by determining the effect of the RNAs on formation of colonies in agar and tumors in mice. (i) Expressing in human melanoma cells the RNA fragments individually promoted tumorigenicity. (ii) Expressing in human melanoma cells a shRNA, which causes degradation of the endogenous RNA from which an RNA fragment was derived, suppressed tumorigenicity. (iii) Expressing in mouse NIH/3T3 cells the RNA fragments individually resulted in transformation to tumorigenic cells. (iv) A screen of 9 human tumor lines showed that each line expresses high levels of several hPSF-binding RNAs, relative to the levels in human fibroblast cells. We conclude that human hPSF-binding RNAs drive transformation and tumorigenesis by reversing PSF-mediated repression of proto-oncogene transcription and that dysfunctional regulation of human hPSF-binding RNA expression has a central role in the etiology of human cancer.