bluuebunny/crossref_metadata_2025 huggingface dataset:
Equatorial and apical solvent shells of the UO22+ ion
Authors: Nichols Patrick , Bylaska Eric J. , Schenter Gregory K. , de Jong Wibe
Published: March 2008

First principles molecular dynamics simulations of the hydration shells surrounding UO22+ ions are reported for temperatures near 300K. Most of the simulations were done with 64 solvating water molecules (22ps). Simulations with 122 water molecules (9ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average UO bond length was found to be 1.77Å. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O–U–O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44Å (2.46Å, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U–O radial distribution function at 4.59Å. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO22+ ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO22+, oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.
A method to increase the Arctic sea ice cover
Authors: Tulaikova Tamara , Osano Minetada , Gladun Anatoly , Amirova Svetlana
Published: March 2008

Proposed in this paper is a new method for preserving the ice in the Arctic regions under the conditions of global warming. The main technique involves artificial polymer films, which are used as an additional cover for the overcooled northern regions. The polymer films are constructed in such a way that they cannot only reflect the incoming solar radiation but also provide additional sites for the nucleation of ice crystals. This feature of polymer films to produce ice crystal aggregation in the larger ice structures in the adjoining area can be achieved by decreasing sea wave amplitudes in the vicinity of the considered area.
Influence of atomic force microscope cantilever tilt and induced torque on force measurements
Authors: Edwards Scott A. , Ducker William A. , Sader John E.
Published: March 2008

Quantitative force measurements performed using the atomic force microscope (AFM) inherently rely on calibration of the AFM cantilever spring constant to convert the measured deflection into a force. Here, we examine the effect of cantilever tilt and induced torque on the effective normal spring constant resulting from variable placement of the tip probe, as is frequently encountered in practice. Explicit general formulas are presented that account for these combined effects for both sharp tips and spherical probes. In contrast to previous studies, we find that induced tip torque can act to either enhance or reduce the effective normal spring constant of the cantilever. The implications of this study to practical force measurements are discussed.
Shape-induced simple cubic arrangement in three-dimensional nanocube self-assemblies
Authors: Yamamuro Saeki , Sumiyama Kenji , Kamiyama Tomoaki
Published: March 2008

The simple cubic packing rarely appears in nature primarily due to its low packing density. Here, we present that the cubic particle shape induces a preferred formation of three-dimensional arrays of simple cubic arrangement, confirmed by transmission electron microscopy and small-angle x-ray scattering. The calculation of van der Waals interaction energy between the particle cores showed that the highly coordinated, simple cubic packing is energetically the most stable, being consistent with the present experimental result.
Electron-nucleus cusp correction and forces in quantum Monte Carlo
Authors: Per Manolo C. , Russo Salvy P. , Snook Ian K.
Published: March 2008

A simple method is presented which ensures the electron-nucleus cusp condition is satisfied by the Slater-Jastrow wavefunctions commonly employed in quantum Monte Carlo simulations. The method is applied in variational energy calculations of the neon atom and a selection of molecules using both Gaussian and Slater basis sets. In addition, we discuss the relationship between the electron-nucleus cusps and the variance of forces, and investigate the sensitivity of forces to the quality of the cusps for various diatomic molecules.
Modified predictive formula for the electron stopping power
Authors: Jablonski A. , Tanuma S. , Powell C. J.
Published: March 2008

We report an improved predictive formula for the electron stopping power (SP) based on an analysis and fit of SPs and electron inelastic mean free paths (IMFPs) calculated from optical data for 37 elemental solids and energies between 200eV and 30keV. The formula is a function of energy, density, and IMFP, and is recommended for solids with atomic numbers larger than 6. While the mean deviation between predicted and calculated SPs was 7.25%, larger deviations were found for four additional materials, Li (22.2%), Be (17.9%), graphite (15.3%), and diamond (15.7%). The predictive SP formula can be applied to multicomponent materials. Test comparisons for two compounds, guanine and InSb, showed average deviations of 16.0% and 19.1%, respectively. The improved SP formula is expected to be useful in simulations of electron trajectories in solids with the continuous slowing-down approximation (e.g., in Auger-electron spectroscopy and electron microprobe analysis).
Oxygen precipitation in Czochralski silicon: Effect of ramped anneal from 300to750°C
Authors: Cui Can , Yang Deren , Ma Xiangyang , Li Ming
Published: March 2008

The effect of ramped anneal (RA) in the temperature range between 300 and 750°C on the formation of oxygen precipitates and their morphology in Czochralski silicon has been investigated. After ramping from 300to750°C at a rate of 1°C∕min, the silicon samples were subjected to a 750°C anneal for 64h. It was found that the RA significantly increased the density of oxygen precipitates and resulted in strongly enhanced oxygen precipitation during the 750°C anneal. A subsequent anneal at 1000°C was carried out to enable further growth of the precipitates. Before and after the 1000°C anneal, the morphology of the oxygen precipitates was investigated by transmission electron microscopy and low temperature Fourier transform infrared spectrometer. This showed that the ramped preanneal also significantly influences the morphology of oxygen precipitates during the subsequent thermal treatment.
Temperature dependence of Raman spectra in single-walled carbon nanotube rings
Authors: Song Li , Ma Wenjun , Ren Yan , Zhou Weiya , Xie Sishen , Tan Pingheng , Sun Lianfeng
Published: March 2008

The temperature-dependent Raman frequency shift in single-walled carbon nanotube (SWCNT) rings in the range of 80–550K is investigated. We observe that the frequency decreases with increasing temperature for all Raman peaks of the nanotube rings. Furthermore, compared to the nanotubes with linear structure, the temperature coefficients of the radial breathing mode and G-mode frequencies of the nanotube rings are much smaller, which means the nanotube rings have more stable thermal ability. We attribute the better thermal stability to the high bending strain energy along the nanotube rings induced by the sidewall curvature.
Field-emission-type x-ray source using carbon-nanofibers
Authors: Kita S. , Watanabe Y. , Ogawa A. , Ogura K. , Sakai Y. , Matsumoto Y. , Isokane Y. , Okuyama F. , Nakazato T. , Otsuka T.
Published: March 2008

An x-ray irradiation system of field-emission type has been constructed using carbon-nanofibers (CNFs) grown on a palladium wire that is 50μm in diameter. The electron current emitted from the CNFs was approximately 1mA and was stable within 10% for a long time t>5000h. The electrons passing through a slit in the gate electrode were accelerated to the desired energy, and were made to impinge on the metal target (Ti, Cu, Mo, and W) for generating x rays. The x-rays transmitted through Be-window were characterized using energy analyzers and a dosimeter. At an acceleration voltage of Va=50kV, the energy spectra of the x-rays were exclusively composed of characteristic signals except for the Mo-target, and the dose rates of x-rays were D=2.5–14Gy∕min, depending on the target metals. This system also provides sharp x-ray images of both biological and nonbiological materials.
The magnetoelectric coefficients of Pb(Fe1/2Nb1/2)O3 and 0.8Pb(Fe1/2Nb1/2)O3−0.2Pb(Mg1/2W1/2)O3
Authors: Levstik A. , Filipič C. , Holc J.
Published: March 2008

The value of the magnetoelectric coefficient γ was estimated for Pb(Fe1/2Nb1/2)O3 and 0.8Pb(Fe1/2Nb1/2)O3−0.2Pb(Mg1/2W1/2)O3 from the measured values of their magnetic susceptibility and remanent polarization.
Anomalous photovoltaic effect in nanocrystalline Si∕SiO2 composites
Authors: Levi Aharoni H. , Azulay D. , Millo O. , Balberg I.
Published: March 2008

We have observed an anomalous photovoltaic effect in films of Si nanocrystals embedded in SiO2. Using conductive-probe atomic force microscopy and global transport measurements, we found, close to the percolation threshold of the Si crystallite phase, a large photovoltaic effect of up to about 7V. Following the dependence of this effect on the size of the Si nanocrystals and on the relative tip position with respect to the counterelectrode, we suggest a model based on charge separation of excited electron-hole pairs governed by the size-dependent quantum confinement and charging energies.
Darboux integrability and algebraic invariant surfaces for the Rikitake system
Authors: Llibre Jaume , Valls Clàudia
Published: March 2008

In this paper, we study the Darboux integrability of the Rikitake system ẋ=−μx+yz, ẏ=−μy+x(z−a), ż=1−xy. More precisely, we characterize all the invariant algebraic surfaces, the exponential factors, and the polynomial, rational, and Darboux first integrals of this system according to the values of its parameters a and μ.
Iron point defect reduction in multicrystalline silicon solar cells
Authors: Pickett Matthew D. , Buonassisi Tonio
Published: March 2008

In this work, we propose and demonstrate an annealing procedure designed to improve the performance of iron-contaminated silicon solar cells. Specifically, we put forward the idea that cells contaminated with iron should be annealed at appropriate times and temperatures to allow for the transformation from supersaturated point defects to distributed iron silicide precipitates. We examine the optimal transformation rate for string ribbon multicrystalline silicon and demonstrate that a 30min annealing can improve the efficiency of cells manufactured from low-purity feedstock.
A charge control analytical model for organic thin film transistors
Authors: Torricelli F. , Kovács-Vajna Zs. M. , Colalongo L.
Published: March 2008

In this paper, a mathematical model for the dc current of organic thin film transistors is proposed. The model is based on the variable range hopping transport theory, while the mathematical expression of the current is formulated by means of the channel accumulation charge. It accurately accounts for below-threshold, linear, and saturation operating conditions via a single formulation and it does not require the explicit definition of the threshold and saturation voltages. Furthermore, thanks to the charge control approach, it is straightforwardly generalizable to dynamic behavior.
1.55
μ
m
GaAs∕GaNAsSb∕GaAs optical waveguides grown by radio frequency nitrogen plasma-assisted molecular beam epitaxy
Authors: Tan K. H. , Yoon S. F. , Loke W. K. , Wicaksono S. , Xu Z. , Ng T. K. , Lew K. L. , Saadsaoud N. , Zegaoui M. , Decoster D. , Chazelas J.
Published: March 2008

We demonstrate a 1.55μm GaAs∕GaNAsSb∕GaAs optical waveguide grown by molecular beam epitaxy as an alternative to the AlGaAs∕GaAs system. The 0.4-μm-thick GaNAsSb guiding layer contains ∼3.5% of N and 9% of Sb, resulting in optical band gap of 0.88eV. The refractive index of the GaNAsSb layer was measured from 800to1700nm. The GaNAsSb layer has a refractive index value of 3.42 at 1.55μm wavelength. The propagation loss measured using the Fabry–Pérot resonance method was found to be affected by nitrogen-related defect absorption.
In situ neutron diffraction study of aligning of crystal orientation in diamagnetic ceramics under magnetic fields
Authors: Terada N. , Suzuki H. S. , Suzuki T. S. , Kitazawa H. , Sakka Y. , Kaneko K. , Metoki N.
Published: March 2008

We have first studied the orientation process of α-Al2O3 fine particles, using in situ neutron diffraction measurements on the particles in a liquid solvent under magnetic fields. The neutron diffraction intensity of 006 and 116 reflections is significantly reduced by the vertical magnetic field up to 100kOe, while the 113 and 204 reflections remain unchanged within the experimental accuracy. The energy balance between the magnetic anisotropic energy and the thermal fluctuation following the Boltzmann distribution is important for the crystal orientation of the α-Al2O3 particles in suspension. Comparing the experimental data with the theoretical equation, we find that the magnetic field, where the particles are fully oriented, is above 200kOe. Our obtained data prove that the in situ neutron diffraction measurement is a powerful tool for investigating the alignment of the crystal orientation under magnetic fields.
Electroluminescence of SnO2∕p-Si heterojunction
Authors: Yuan Zhizhong , Li Dongsheng , Wang Minghua , Chen Peiliang , Gong Daoren , Cheng Peihong , Yang Deren
Published: March 2008

Polycrystalline SnO2 film of tetragonal rutile structure with an optical band gap of 3.9eV was formed by oxidation process at 1000°C on electron beam evaporation deposited Sn film. Room temperature electroluminescence from the SnO2∕p-Si heterojunction was observed at 590nm when the device was under sufficient forward bias with the positive voltage applied on the p-Si substrate. It is proposed that the electrons in the conduction band of SnO2 relax to defect states that resulted from the dangling bonds at the surface of the small SnO2 grains and then radiatively recombine with the holes in the valence band.
Size induced arrest of the room temperature crystallographic structure in nanoparticles of La0.5Ca0.5MnO3
Authors: Sarkar Tapati , Raychaudhuri A. K. , Chatterji Tapan
Published: March 2008

We have shown, using high resolution x-ray diffraction studies of nanoparticles, that size reduction can lead to an arrest of the high temperature phase in perovskite materials, which prevents growth of the low temperature phase that needs a specific crystal structure for its stabilization. This has been shown in the context of ∼15nm diameter nanocrystals of La0.5Ca0.5MnO3, in which the orthorhombic distortion at room temperature freezes in and, as a consequence, the charge order cannot set in and the ferromagnetic state that sets in at higher temperature is stabilized at low temperature.
SME Policy Support in Britain since the 1990s: What have We Learnt?
Authors: Bennett Robert
Published: March 2008

I examine the evolution of British government support to small and medium-sized enterprises (SMEs), using results from four waves of survey evidence in 1991, 1997, 2002, and 2004, and comparison with other analyses. Whilst government support is often based on overcoming market failures in the availability or use of supports to SMEs, I argue that successful government intervention is difficult to make effective at realistic cost – benefit ratios. The analysis demonstrates little evidence of market failure in provision or take-up of business support. If a market gap existed in the past, it is no longer apparent. Any systemic market failures that remain can influence only the start-up, very early stage growth, and/or the very smallest single-person businesses. I also find that different modes of delivery by centralised, regionalised, or localised structures have very little influence on market penetration. Decentralisation can increase take-up marginally, but this has been achieved only with tenfold increases in costs and major increases in administrative complexity. There is some marginal but significant benefit of policy delivery being in the hands of market, or near-market, agencies. But for all delivery bodies there is massive variability in use, impact, and satisfaction levels achieved. Finally, a brief analysis of gender differences suggests some significant variations in use of advice from different sources, but that government sources have some of the most adverse use levels for female-headed business, and this particularly applies to Business Link. Over the period 1991 – 2004 there is little to indicate the overwhelming success of government SME support policies, particularly at the level of cost that they now involve.
Constructing Female Entrepreneurship Policy in the UK: Is the US a Relevant Benchmark?
Authors: Marlow Susan , Carter Sara , Shaw Eleanor
Published: March 2008

Successive UK governments have introduced a range of policy initiatives designed to encourage more women to start new firms. Underpinning these policies has been an explicit ambition for the UK to achieve similar participation rates as those in the US where it is widely reported that women own nearly half the stock of businesses. The data underlying these objectives are critically evaluated and it is argued that the definitions and measures of female enterprise used in the UK and the US restrict meaningful comparisons between the two. It is suggested that the expansion of female entrepreneurship in the US is historically and culturally specific to that country. UK policy goals should reflect the national socioeconomic context, while drawing upon good practice examples from a range of other countries. The paper concludes by discussing the economic and social viability of encouraging more women in the UK to enter self-employment without fully recognising the intensely competitive sectors in which they are often located.
Toward a Philosophy of the Urban: Henri Lefebvre's Uncomfortable Application of Bergsonism
Authors: Fraser Benjamin
Published: March 2008

Although Henri Lefebvre (1901–1991) publicly and consistently eschewed the philosophy of Henri Bergson (1859–1941), his writings in effect made great use of the latter's key ideas and method. Like Bergson's philosophy, Lefebvre's urban criticism denounced the spatialization of time and gave priority to lived experience over the abstractions employed by static intellectual or traditionally analytical models of experience. Throughout The Urban Revolution, The Production of Space, The Critique of Everyday Life, Volumes 1–3, and the writings posthumously collected in Rhythmanalysis, Lefebvre's urban philosophical project appropriated the ideas Bergson advanced in his three major works, Time and Free Will, Matter and Memory, and Creative Evolution, through their application to the problems of social life—a de facto collaboration that Bergson never lived to appreciate and that Lefebvre would never recognize. This connection is important not only as a corrective to the scant attention paid to Lefebvre's work by philosophers, but also because it reinforces both thinkers' own emphases on interdisciplinarity and on reconciling theories of knowledge with theories of life. The combined work of the two philosophers suggests a philosophical basis for the current emphasis of theory in both cultural studies and human geography in that it stresses the importance of acknowledging movement, process, and mobilities in approaches to the problems of urban life. The composite of Bergson–Lefebvre provides the basis for articulating a philosophy of the urban.
Crystal structure of DNA-bound Co(III)·bleomycin B
2
: Insights on intercalation and minor groove binding
Authors: Goodwin Kristie D. , Lewis Mark A. , Long Eric C. , Georgiadis Millie M.
Published: March 2008

Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cleaving chemotherapeutic agents. The bleomycins consist of a disaccharide-modified metal-binding domain connected to a bithiazole/C-terminal tail via a methylvalerate-Thr linker and induce DNA damage after oxygen activation through site-selective cleavage of duplex DNA at 5′-GT/C sites. Here, we present crystal structures of two different 5′-GT containing oligonucleotides in both the presence and absence of bound Co(III)·bleomycin B
2
. Several findings from our studies impact the current view of bleomycin binding to DNA. First, we report that the bithiazole intercalates in two distinct modes and can do so independently of well ordered minor groove binding of the metal binding/disaccharide domains. Second, the Co(III)-coordinating equatorial ligands in our structure include the imidazole, histidine amide, pyrimidine N1, and the secondary amine of the β aminoalanine, whereas the primary amine acts as an axial ligand. Third, minor groove binding of Co(III)·bleomycin involves direct hydrogen bonding interactions of the metal binding domain and disaccharide with the DNA. Finally, modeling of a hydroperoxide ligand coordinated to Co(III) suggests that it is ideally positioned for initiation of C4′-H abstraction.
Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-Å structure of the heparin-bridged complex
Authors: Li Wei , Adams Ty E. , Nangalia Jyoti , Esmon Charles T. , Huntington James A.
Published: March 2008

Protein C inhibitor (PCI) is a serpin with many roles in biology, including a dual role as pro- and anticoagulant in blood. The protease specificity and local function of PCI depend on its interaction with cofactors such as heparin-like glycosaminoglycans (GAGs) and thrombomodulin (TM). Both cofactors significantly increase the rate of thrombin inhibition, but GAGs serve to promote the anticoagulant activity of PCI, and TM promotes its procoagulant function. To gain insight into how PCI recognition of thrombin is aided by these cofactors, we determined a crystallographic structure of the Michaelis complex of PCI, thrombin, and heparin to 1.6 Å resolution. Thrombin interacts with PCI in an unusual fashion that depends on the length of PCI's reactive center loop (RCL) to align the heparin-binding sites of the two proteins. The principal exosite contact is engendered by movement of thrombin's 60-loop in response to the unique P2 Phe of PCI. This mechanism of communication between the active site of thrombin and its recognition exosite is previously uncharacterized and may relate to other thrombin substrate–cofactor interactions. The cofactor activity of heparin thus depends on the formation of a heparin-bridged Michaelis complex and substrate-induced exosite contacts. We also investigated the cofactor effect of TM, establishing that TM bridges PCI to thrombin through additional direct interactions. A model of the PCI–thrombin–TM complex was built and evaluated by mutagenesis and suggests distinct binding sites for heparin and TM on PCI. These data significantly improve our understanding of the cofactor-dependent roles of PCI in hemostasis.
Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle
Authors: Sedaghat Ahmad R. , Dinoso Jason B. , Shen Lin , Wilke Claus O. , Siliciano Robert F.
Published: March 2008

The time to suppression of HIV-1 viremia to below the limit of detection of standard clinical assays is an important prognostic indicator for patients on highly active antiretroviral therapy (HAART). Recent clinical trials of the integrase inhibitor raltegravir have demonstrated more rapid viral decay than previously seen with reverse transcriptase (RT) or protease inhibitor-based regimens. Because of the therapeutic importance of drugs that target different steps in the virus life cycle, it is imperative to consider whether viral dynamics are affected by the stage of the viral life cycle at which an antiretroviral drug acts. We use a mathematical model to investigate the effects of various drug classes on the dynamics of HIV-1 decay and show that the stage at which a drug acts affects the dynamics of viral decay. We find that the drug class acting latest in the viral life cycle dictates the dynamics of HIV-1 decay. In general, we find that the later in the life cycle an inhibitor acts, the more rapid the decay in viremia, and we illustrate this by comparing the effect of RT and integrase inhibitors on viral dynamics. We conclude that the rapid decay observed in patients on integrase-inhibitor-containing regimens is not necessarily an indication of greater drug efficacy but rather an expected consequence of the fact that this drug acts later in the life cycle. We propose that clinically observed viral decay rates for HAART regimens should be evaluated in the context of the drug classes that are represented.
Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the
Escherichia coli
ammonia channel AmtB
Authors: Javelle Arnaud , Lupo Domenico , Ripoche Pierre , Fulford Tim , Merrick Mike , Winkler Fritz K.
Published: March 2008

The conduction mechanism of
Escherichia coli
AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic “gate” formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH
4
+
deprotonation takes place at S1 before NH
3
conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport.
Amino acid copolymer-specific IL-10-secreting regulatory T cells that ameliorate autoimmune diseases in mice
Authors: Stern Joel N. H. , Keskin Derin B. , Zhang Hong , Lv HuiJuan , Kato Zenichiro , Strominger Jack L.
Published: March 2008

IL-10-secreting regulatory T cell lines specific to glatiramer acetate [poly(Y,E,A,K)n] or poly(Y,F,A,K)n have been established from the enlarged spleen and lymph nodes that result from copolymer treatment of SJL mice in which experimental autoimmune encephalomyelitis was induced by PLP139-151. These CD4+CD25+T cell lines secrete high levels of IL-10 and IL-13 but only small amounts of IL-4 and virtually no TGF-β, IL-17, IL-6, IFN-γ, or TNF-α. Their phenotypes are particularly characterized by the absence of Foxp3 and the presence of two TNFR family members, CD30 and GITR. The lines proliferated specifically to the immunizing copolymers but were autoantigen-nonspecific, in that the same T cell line could suppress autoimmunity induced by three different autoantigens in SJL mice, i.e., PLP139-151(EAE), MBP85-99 (EAE), and bovine peripheral nerve myelin (experimental autoimmune neuritis), indicating they function by bystander suppression.
Three thioredoxin targets in the inner envelope membrane of chloroplasts function in protein import and chlorophyll metabolism
Authors: Bartsch Sandra , Monnet Julie , Selbach Kristina , Quigley Françoise , Gray John , von Wettstein Diter , Reinbothe Steffen , Reinbothe Christiane
Published: March 2008

Thioredoxins (Trxs) are ubiquitous small proteins with a redox-active disulfide bridge. In their reduced form, they constitute very efficient protein disulfide oxidoreductases. In chloroplasts, two types of Trxs (
f
and
m
) coexist and play central roles in the regulation of the Calvin cycle and other processes. Here, we identified a class of Trx targets in the inner plastid envelope membrane of chloroplasts that share a CxxC motif ≈73 aa from their carboxyl-terminal end. Members of this group belong to a superfamily of Rieske iron–sulfur proteins involved in protein translocation and chlorophyll metabolism. These proteins include the protein translocon protein TIC55, the precursor NADPH:protochlorophyllide oxidoreductase translocon protein PTC52, which operates as protochlorophyllide
a
-oxygenase, and the lethal leaf spot protein LLS1, which is identical with pheophorbide
a
oxygenase. The role of these proteins in dark/light regulation and oxidative control by the Trx system is discussed.
Cyclosporin A corrects mitochondrial dysfunction and muscle apoptosis in patients with collagen VI myopathies
Authors: Merlini Luciano , Angelin Alessia , Tiepolo Tania , Braghetta Paola , Sabatelli Patrizia , Zamparelli Alessandra , Ferlini Alessandra , Maraldi Nadir M. , Bonaldo Paolo , Bernardi Paolo
Published: March 2008

Ullrich congenital muscular dystrophy and Bethlem myopathy are skeletal muscle diseases that are due to mutations in the genes encoding collagen VI, an extracellular matrix protein forming a microfibrillar network that is particularly prominent in the endomysium of skeletal muscle. Myoblasts from patients affected by Ullrich congenital muscular dystrophy display functional and ultrastructural mitochondrial alterations and increased apoptosis due to inappropriate opening of the permeability transition pore, a mitochondrial inner membrane channel. These alterations could be normalized by treatment with cyclosporin A, a widely used immunosuppressant that desensitizes the permeability transition pore independently of calcineurin inhibition. Here, we report the results of an open pilot trial with cyclosporin A in five patients with collagen VI myopathies. Before treatment, all patients displayed mitochondrial dysfunction and increased frequency of apoptosis, as determined in muscle biopsies. Both of these pathologic signs were largely normalized after 1 month of oral cyclosporin A administration, which also increased muscle regeneration. These findings demonstrate that collagen VI myopathies can be effectively treated with drugs acting on the pathogenic mechanism downstream of the genetic lesion, and they represent an important proof of principle for the potential therapy of genetic diseases.
Extreme resistance of bdelloid rotifers to ionizing radiation
Authors: Gladyshev Eugene , Meselson Matthew
Published: March 2008

Rotifers of class Bdelloidea are common invertebrate animals with highly unusual characteristics, including apparently obligate asexuality, the ability to resume reproduction after desiccation at any life stage, and a paucity of transposable genetic elements of types not prone to horizontal transmission. We find that bdelloids are also extraordinarily resistant to ionizing radiation (IR). Reproduction of the bdelloidsAdineta vagaandPhilodina roseolais much more resistant to IR than that ofEuchlanis dilatata, a rotifer belonging to the desiccation-intolerant and facultatively sexual class Monogononta, and all other animals for which we have found relevant data. By analogy with the desiccation- and radiation-resistant bacteriumDeinococcus radiodurans, we suggest that the extraordinary radiation resistance of bdelloid rotifers is a consequence of their evolutionary adaptation to survive episodes of desiccation encountered in their characteristic habitats and that the damage incurred in such episodes includes DNA breakage that is repaired upon rehydration. Such breakage and repair may have maintained bdelloid chromosomes as colinear pairs and kept the load of transposable genetic elements low and may also have contributed to the success of bdelloid rotifers in avoiding the early extinction suffered by most asexuals.
Identification of noninvasive imaging surrogates for brain tumor gene-expression modules
Authors: Diehn Maximilian , Nardini Christine , Wang David S. , McGovern Susan , Jayaraman Mahesh , Liang Yu , Aldape Kenneth , Cha Soonmee , Kuo Michael D.
Published: March 2008

Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor in adults. We combined neuroimaging and DNA microarray analysis to create a multidimensional map of gene-expression patterns in GBM that provided clinically relevant insights into tumor biology. Tumor contrast enhancement and mass effect predicted activation of specific hypoxia and proliferation gene-expression programs, respectively. Overexpression of EGFR, a receptor tyrosine kinase and potential therapeutic target, was also directly inferred by neuroimaging and was validated in an independent set of tumors by immunohistochemistry. Furthermore, imaging provided insights into the intratumoral distribution of gene-expression patterns within GBM. Most notably, an “infiltrative” imaging phenotype was identified that predicted patient outcome. Patients with this imaging phenotype had a greater tendency toward having multiple tumor foci and demonstrated significantly shorter survival than their counterparts. Our findings provide an
in vivo
portrait of genome-wide gene expression in GBM and offer a potential strategy for noninvasively selecting patients who may be candidates for individualized therapies.
The structure of LepA, the ribosomal back translocase
Authors: Evans Robin N. , Blaha Gregor , Bailey Scott , Steitz Thomas A.
Published: March 2008

LepA is a highly conserved elongation factor that promotes the back translocation of tRNAs on the ribosome during the elongation cycle. We have determined the crystal structure of LepA from
Escherichia coli
at 2.8-Å resolution. The high degree of sequence identity between LepA and EF-G is reflected in the structural similarity between the individual homologous domains of LepA and EF-G. However, the orientation of domains III and V in LepA differs from their orientations in EF-G. LepA also contains a C-terminal domain (CTD) not found in EF-G that has a previously unobserved protein fold. The high structural similarity between LepA and EF-G enabled us to derive a homology model for LepA bound to the ribosome using a 7.3-Å cryo-EM structure of a complex between EF-G and the 70S ribosome. In this model, the very electrostatically positive CTD of LepA is placed in the direct vicinity of the A site of the large ribosomal subunit, suggesting a possible interaction between the CTD and the back translocated tRNA or 23S rRNA.
Alternative splicing of the G protein-coupled receptor superfamily in human airway smooth muscle diversifies the complement of receptors
Authors: Einstein Richard , Jordan Heather , Zhou Weiyin , Brenner Michael , Moses Esther G. , Liggett Stephen B.
Published: March 2008

G protein-coupled receptors (GPCRs) are the largest signaling family in the genome, serve an expansive array of functions, and are targets for ≈50% of current therapeutics. In many tissues, such as airway smooth muscle (ASM), complex, unexpected, or paradoxical responses to agonists/antagonists occur without known mechanisms. We hypothesized that ASM express many more GPCRs than predicted, and that these undergo substantial alternative splicing, creating a highly diversified receptor milieu. Transcript arrays were designed detecting 434 GPCRs and their predicted splice variants. In this cell type, 353 GPCRs were detected (including 111 orphans), with expression levels varying by ≈900-fold. Receptors used for treating airway disease were expressed lower than others with similar signaling properties, indicating potentially more effective targets. A disproportionate number of Class-A peptide-group receptors, and those coupling to G
q
/
11
or G
s
(vs. G
i
), was found. Importantly, 192 GPCRs had, on average, five different expressed receptor isoforms because of splicing events, including alternative splice donors and acceptors, novel introns, intron retentions, exon(s) skips, and novel exons, with the latter two events being most prevalent. The consequences of splicing were further investigated with the leukotriene B4 receptor, known for its aberrant responsiveness in lung. We found transcript expression of three variants because of alternative donor and acceptor splice sites, representing in-frame deletions of 38 and 100 aa, with protein expression of all three isoforms. Thus, alternative splicing, subject to conditional, temporal, and cell-type regulation, is a major mechanism that diversifies the GPCR superfamily, creating local recepteromes with specialized environments.
Needle tract seeding after vacuum-assisted breast biopsy
Authors: Michalopoulos N. V. , Zagouri F. , Sergentanis T. N. , Pararas N. , Koulocheri D. , Nonni A. , Filippakis G. M. , Chatzipantelis P. , Bramis J. , Zografos G. C.
Published: March 2008

Background: A matter of substantial concern regarding all needle biopsy techniques is seeding along the biopsy needle tract.

Purpose: To assess cell seeding along the needle tract of vacuum-assisted breast biopsy (VABB).

Material and Methods: The study included 21 patients with ductal carcinoma in situ (DCIS) and 10 patients with invasive ductal carcinoma (IDC) diagnosed by VABB for nonpalpable mammographic lesions. VABB (11G, on a Fischer table) was performed, and the duration of the procedure was measured. After surgery, the whole needle tract was embedded in paraffin blocks, stained with hematoxylin-eosin, and examined by a pathologist.

Results: Cases with dissemination of cancer cells in the needle tract were not observed (one-sided 97.5% CI 0–10.0%). In 2/31 (6.5%) cases (95% CI 0.8–21.4%), benign epithelial cell displacement was observed, and the duration of VABB was significantly longer in these two cases (52.5±3.5 min vs. 42.0±4.4 min for cases without benign cell displacement; P = 0.018, Mann-Whitney-Wilcoxon test for independent samples).

Conclusion: No displacement of malignant cells within the 11G needle tract was documented. Benign cell displacement was associated with longer VABB duration. The phenomenon of tumor cell dissemination along the needle tract is of questionable clinical significance when the treatment guidelines are followed.
Role of scintigraphy with technetium-99m depreotide in the diagnosis and management of patients with suspected lung cancer
Authors: Axelsson R. , Herlin G. , Bååth M. , Aspelin P. , Kölbeck K. G.
Published: March 2008

Background: In Sweden, there are over 3000 new lung cancer cases every year. There are still numerous patients with undetermined lesions after routine diagnostic evaluation by clinical examination, chest radiography, computed tomography (CT) of the thorax, and bronchoscopy. An appropriate method for further diagnostic workup is therefore needed.

Purpose: To evaluate the diagnostic value of the somatostatin analogue depreotide in patients with suspected lung cancer, and to determine in which clinical settings it would be beneficial to use 99mTc-depreotide scintigraphy.

Material and Methods: We included 99 consecutive patients referred to our hospital with suspected lung cancer. A clinical examination, bronchoscopy, chest radiography, CT of the thorax and upper abdomen, and scintigraphy were done. Scintigraphy was performed after injection of 740 MBq 99mTc depreotide with tomographical imaging of the thorax and whole-body scanning. The diagnostic outcome of the scintigrams was compared to CT, using morphology or clinical outcome as the endpoint.

Results:99mTc-depreotide uptake was found in 62 out of 66 malignancies, including 57 of 58 primary lung cancer cases. Two cases of lung metastasis (one from a colon cancer and one from an adenoid cystic carcinoma originating in the palate) and one rib chondrosarcoma did not show depreotide uptake. There were 33 patients with benign lesions, of whom 16 displayed false-positive 99mTc-depreotide uptake, whereof 11 were pneumonias. Tc-99m-depreotide uptake was absent in 17 patients with benign lesions, including all 10 hamartomas. The sensitivity in detecting malignancy was 94%, and in detecting lung cancer 98%. The specificity was calculated based on two sets of data. When all cases were used, the specificity was 52%. If the 12 pneumonias are excluded, the specificity was 77%.

Conclusion:99mTc-depreotide scintigraphy has a high sensitivity in detecting lung cancer. The method is useful in decision-making with respect to surgery.
Nutrition, sleep and recovery
Authors: Halson Shona L.
Published: March 2008

Ensuring athletes achieve an appropriate quality and/or quantity of sleep may have significant implications for performance and recovery and reduce the risk of developing overreaching or overtraining. Indeed, sleep is often anecdotally suggested to be the single best recovery strategy available to elite athletes. A number of nutritional factors have been suggested to improve sleep, including valerian, melatonin, tryptophan, a high glycaemic index diet before bedtime, and maintenance of a balanced and healthy diet. Conversely, consumption of alcohol and caffeine and hyper‐hydration may disturb sleep. Strategies such as warming the skin, hydrotherapy, and adoption of appropriate sleep hygiene (maintenance of good sleep habits and routines) are other tools to aid in sleep promotion. Ensuring athletes gain an appropriate quality and quantity of sleep may be important for optimal athletic performance.
Creationism and Intelligent Design
Authors: Lurquin Paul F. , Stone Linda
Published: March 2008

This chapter demonstrates that Intelligent Design can be called a form of neocreatonism that, just like old-style creationism, confuses the word “theory” with the words “postulate” and “fact”. It shows that Intelligent Design implies purpose in the universe, a concept that science can neither support nor refute. It further describes creation myths as found in Buddhism, Hinduism, Islam, and Judaism, discussing how these myths influence scientific thinking in various societies.
The effects of surfactant on the multiscale structure of bubbly flows
Authors: Takagi Shu , Ogasawara Toshiyuki , Matsumoto Yoichiro
Published: March 2008

It is well known that a bubble in contaminated water rises much slower than one in purified water, and the rising velocity in a contaminated system can be less than half that in a purified system. This phenomenon is explained by the so-called Marangoni effect caused by surfactant adsorption on the bubble surface. In other words, while a bubble is rising, there exists a surface concentration distribution of surfactant along the bubble surface because the adsorbed surfactant is swept off from the front part and accumulates in the rear part by advection. Owing to this surfactant accumulation in the rear part, a variation of surface tension appears along the surface and this causes a tangential shear stress on the bubble surface. This shear stress results in the decrease in the rising velocity of the bubble in contaminated liquid. More interestingly, this Marangoni effect influences not only the bubble's rising velocity but also its lateral migration in the presence of mean shear. Together, these influences cause a drastic change of the whole bubbly flow structures. In this paper, we discuss some experimental results related to this drastic change in bubbly flow structure. We show that bubble clustering phenomena are observed in an upward bubbly channel flow under certain conditions of surfactant concentrations. This cluster disappears with an increase in the concentration. We explain this phenomenon by reference to the lift force acting on a bubble in aqueous surfactant solutions. It is shown that the shear-induced lift force acting on a contaminated bubble of 1 mm size can be much smaller than that on a clean bubble.
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Authors: Zerbino Daniel R. , Birney Ewan
Published: March 2008

We have developed a new set of algorithms, collectively called “Velvet,” to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25–50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of ∼8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
Cellulose Synthesis inPhytophthora infestansIs Required for Normal Appressorium Formation and Successful Infection of Potato
Authors: Grenville-Briggs Laura J. , Anderson Victoria L. , Fugelstad Johanna , Avrova Anna O. , Bouzenzana Jamel , Williams Alison , Wawra Stephan , Whisson Stephen C. , Birch Paul R.J. , Bulone Vincent , van West Pieter
Published: March 2008

Cellulose, the important structural compound of cell walls, provides strength and rigidity to cells of numerous organisms. Here, we functionally characterize four cellulose synthase genes (CesA) in the oomycete plant pathogen Phytophthora infestans, the causal agent of potato (Solanum tuberosum) late blight. Three members of this new protein family contain Pleckstrin homology domains and form a distinct phylogenetic group most closely related to the cellulose synthases of cyanobacteria. Expression of all four genes is coordinately upregulated during pre- and early infection stages of potato. Inhibition of cellulose synthesis by 2,6-dichlorobenzonitrile leads to a dramatic reduction in the number of normal germ tubes with appressoria, severe disruption of the cell wall in the preinfection structures, and a complete loss of pathogenicity. Silencing of the entire gene family in P. infestans with RNA interference leads to a similar disruption of the cell wall surrounding appressoria and an inability to form typical functional appressoria. In addition, the cellulose content of the cell walls of the silenced lines is >50% lower than in the walls of the nonsilenced lines. Our data demonstrate that the isolated genes are involved in cellulose biosynthesis and that cellulose synthesis is essential for infection by P. infestans.
Serological response against Mycobacterium avium complex glycolipid antigens in patients with acquired immunodeficiency syndrome
Authors: Ashino Yugo , Guio Heinner , Iwamoto Aikichi , Yano Ikuya , Matsumura Takeshi , Hattori Toshio
Published: March 2008

In 43 MAC infected patients (23 non‐HIV and 20 AIDS) the IgG response against 3 BCG and 2 MAC antigens was assessed. The response to four antigens in patients with AIDS was considerably lower than in non‐HIV infected patients. Therefore, antibody production against MAC glycolipid antigens was impaired in AIDS patients.