bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of outer-sphere dipolar time correlation functions from high-field NMR measurements. Example of a Gd3+ complex in a viscous solvent
Authors: Fries Pascal H. , Imbert Daniel , Melchior Andrea
Published: January 2010

We consider a diamagnetic species carrying a nuclear spin and having a purely outer-sphere dynamics with respect to a Gd3+ complex. The maximal structural and dynamic information attainable from the paramagnetic relaxation (rate) enhancement (PRE) of this nuclear spin due to the Gd3+ electronic spin is the outer-sphere dipolar time correlation function (OS-DTCF) of the relative position of these spins. We show how to determine this OS-DTCF by a model-free analysis of high-field PRE measurements, which accounts for the relative diffusion coefficient of the spin carrying species derived from pulsed-gradient spin-echo experiments. The method rests on the spectral characterization of the OS-DTCF through a PRE property, the “star” relaxivity, which can be measured over an unexpectedly large frequency range by combining multiple field and temperature NMR experiments. It is illustrated in the case of the H1 spins on the three diamagnetic probes tert-butanol CHD2(CD3)2COD and glycerol (CD2OD)2CHOD and CHDOD–CDOD–CD2OD interacting with Gddtpa2− (dtpa5−=diethylen triamin pentaacetate) in a viscous glycerol-d8/D2O solvent. The general usefulness of the OS-DTCF for the description of the liquid state and electronic spin relaxation is discussed.
An underlap field-effect transistor for electrical detection of influenza
Authors: Lee Kwang-Won , Choi Sung-Jin , Ahn Jae-Hyuk , Moon Dong-Il , Park Tae Jung , Lee Sang Yup , Choi Yang-Kyu
Published: January 2010

An underlap channel-embedded field-effect transistor (FET) is proposed for label-free biomolecule detection. Specifically, silica binding protein fused with avian influenza (AI) surface antigen and avian influenza antibody (anti-AI) were designed as a receptor molecule and a target material, respectively. The drain current was significantly decreased after the binding of negatively charged anti-AI on the underlap channel. A set of control experiments supports that only the biomolecules on the underlap channel effectively modulate the drain current. With the merits of a simple fabrication process, complementary metal-oxide-semiconductor compatibility, and enhanced sensitivity, the underlap FET could be a promising candidate for a chip-based biosensor.
Nanoscale properties of thin twin walls and surface layers in piezoelectric WO3−x
Authors: Kim Yunseok , Alexe Marin , Salje Ekhard K. H.
Published: January 2010

Reduced WO3 single crystals have been investigated by conductive and piezoresponse force microscopy. The reduced crystals show a piezoelectric active surface layer with a noncentrosymmetric tetragonal structure which is different from the bulk of the crystal. The domain walls carry a high current while the bulk remains insulating. Twin-related interfaces are atomically thin, the upper bound being less than 10 nm. The reduced surface layer remained in the piezoelectric state even after several weeks, while the current in the twin boundaries was reduced by re-oxidization. This layer shows a significant piezoelectric activity with a piezoelectric coefficient of about 7.9 pm/V.
Jahn–Teller distortion of ionized and excited carbon nanotubes
Authors: Szakács Péter , Kocsis Dorina , Surján Péter R.
Published: January 2010

Due to their rotational (Cn) symmetry, neutral zigzag and armchair type nanotubes possess doubly degenerate orbitals. As the energies of highest occupied molecular orbital and lowest unoccupied molecular orbital are usually different, neutral nanotubes exhibit a nondegenerate ground state. Ionized or excited forms of these tubes, however, may undergo Jahn–Teller distortion if degenerate orbitals show up in the vicinity of the Fermi level. Theoretical calculations in a simple one-eletron-per-site model show that the Jahn–Teller distortion energies are in order-of-magnitude of 0.1 eV for short pieces of tubes, and are associated with a significant geometry change. Distortions tend to diminish quickly with increasing tube length, except if multiple ionizations are considered.
High quality single shot diffraction patterns using ultrashort megaelectron volt electron beams from a radio frequency photoinjector
Authors: Musumeci P. , Moody J. T. , Scoby C. M. , Gutierrez M. S. , Bender H. A. , Wilcox N. S.
Published: January 2010

Single shot diffraction patterns using a 250-fs-long electron beam have been obtained at the UCLA Pegasus laboratory. High quality images with spatial resolution sufficient to distinguish closely spaced peaks in the Debye–Scherrer ring pattern have been recorded by scattering the 1.6 pC 3.5 MeV electron beam generated in the rf photoinjector off a 100-nm-thick Au foil. Dark current and high emittance particles are removed from the beam before sending it onto the diffraction target using a 1 mm diameter collimating hole. These results open the door to the study of irreversible phase transformations by single shot MeV electron diffraction.
Microdisplacement sensor using an optically trapped microprobe based on the interference scale
Authors: Michihata Masaki , Hayashi Terutake , Nakai Daisuke , Takaya Yasuhiro
Published: January 2010

Positioning technology is one of the most important technologies for developing microsystems. In particular, displacement sensors are necessary for positioning devices with nanoscale accuracy. In this study, we propose a new displacement sensor that uses an interference scale as a linear scale and a laser-trapped microsphere as a sensing probe. This sensor has a wide measuring range, high resolution, and accessibility for narrow target areas. A glass microsphere was optically trapped by means of the laser trapping technique. Between the target surface and the probe, an interference scale was generated along the optical axis. The scale origin was fixed on the target surface. The distance between the probe and the target surface could be measured in terms of the shift in the interference scale. This study investigated the fundamental performance of the sensor. The resolution and accuracy of the sensor were 10 and ±50 nm, respectively; these values could be improved by using trapping lasers having shorter wavelengths. The measurable range was 250 μm. This sensor can provide useful displacement information from a target area having dimensions smaller than 15 μm. In addition, the displacement sensor can measure the distance even for surfaces inclined at angles less than 15°; thus, a flexible arrangement can be used to carry out measurements. In addition, the direction of displacement can be identified.
Guided nucleation of superconductivity on a graded magnetic substrate
Authors: Milošević M. V. , Gillijns W. , Silhanek A. V. , Libál A. , Peeters F. M. , Moshchalkov V. V.
Published: January 2010

We demonstrate the controlled spatial nucleation of superconductivity in a thin film deposited on periodic arrays of ferromagnetic dots with gradually increasing diameter. The perpendicular magnetization of the dots induces vortex-antivortex molecules in the sample, with the number of (anti)vortices increasing with magnet size. The resulting gradient of antivortex density between the dots predetermines local nucleation of superconductivity in the sample as a function of the applied external field and temperature. In addition, the compensation between the applied magnetic field and the antivortices results in an unprecedented enhancement of the critical temperature.
Physical device modeling of carbon nanotube/GaAs photovoltaic cells
Authors: Li Hong , Loke Wan Khai , Zhang Qing , Yoon S. F.
Published: January 2010

Photovoltaic response from semiconducting single-walled carbon nanotubes/n-type GaAs heterojunctions has been investigated. We propose a detailed device model of the photovoltaic cell, in which electron transport can be described as follows. The thermionic emission and tunneling through the spike barrier caused by the conduction band discontinuity dominate electron transport under a low and high-forward bias, respectively. In contrast, the dominant transport mechanisms at low and high-reverse bias could be attributed to the direct and Fowler–Nordheim tunneling though a molecular junction, respectively. Within this framework, the current-voltage characteristics of the photovoltaic response can be quantitatively described.
Slow-light-enhanced single quantum dot emission in a unidirectional photonic crystal waveguide
Authors: Dewhurst S. J. , Granados D. , Ellis D. J. P. , Bennett A. J. , Patel R. B. , Farrer I. , Anderson D. , Jones G. A. C. , Ritchie D. A. , Shields A. J.
Published: January 2010

We report the observation of a Purcell enhancement of the in-plane spontaneous emission rates of InAs self-assembled quantum dots coupled to a mode of a unidirectional photonic crystal waveguide fabricated in GaAs(001). Three-dimensional finite-difference time-domain simulations predict the existence of high quality-factor modes due to the slow light resonances of the waveguide. These modes have been observed experimentally with microphotoluminescence and produce enhanced in-plane emission when resonant with a quantum dot.
Recoverable electroluminescence from a contaminated organic/organic interface in an organic light-emitting diode
Authors: Liao L. S. , Klubek K. P. , Madathil J. K. , Tang C. W. , Giesen D. J.
Published: January 2010

An organic/organic interface, like an electrode/organic interface in an organic light-emitting diode (OLED), can be severely affected by ambient contamination. However, we surprisingly found that the contaminated surface or interface can be “cured” by depositing a thin interfacial layer containing a strong reducing agent onto the contaminated surface before finishing the fabrication of the device. For example, in comparison with a regular OLED, an OLED having a 5-min ambient exposure to the light-emitting layer/electron-transporting layer interface drops its initial electroluminescence (EL) intensity by 50%. The decreased EL intensity due to the 5-min ambient exposure can be fully recovered and the improved operational stability can be realized after curing the contaminated interface using a thin Li interfacial layer. The experimental results provide a useful method to cope with the interfacial contamination in OLEDs during a manufacturing process. In addition, our results support the failure mechanism of an Alq-based OLED suggested by [Papadimitrakopoulos et al., Chem. Mater. 8, 1363 (1996)].
Communications: Can one identify nonequilibrium in a three-state system by analyzing two-state trajectories?
Authors: Amann Christian P. , Schmiedl Tim , Seifert Udo
Published: January 2010

For a three-state Markov system in a stationary state, we discuss whether, on the basis of data obtained from effective two-state (or on-off) trajectories, it is possible to discriminate between an equilibrium state and a nonequilibrium steady state. By calculating the full phase diagram we identify a large region where such data will be consistent only with nonequilibrium conditions. This regime is considerably larger than the region with oscillatory relaxation, which has previously been identified as a sufficient criterion for nonequilibrium.
AlN/GaN double-barrier resonant tunneling diodes grown by metal-organic chemical vapor deposition
Authors: Bayram C. , Vashaei Z. , Razeghi M.
Published: January 2010

AlN/GaN double-barrier resonant tunneling diodes (RTDs) were grown by metal-organic chemical vapor deposition on sapphire. RTDs were fabricated via standard processing steps. RTDs demonstrate a clear negative differential resistance (NDR) at room temperature (RT). The NDR was observed around 4.7 V with a peak current density of 59 kA/cm2 and a peak-to-valley ratio of 1.6 at RT. Dislocation-free material is shown to be the key for the performance of GaN RTDs.
Photonic crystal cavities in silicon dioxide
Authors: Gong Yiyang , Vučković Jelena
Published: January 2010

One dimensional nanobeam photonic crystal cavities fabricated in silicon dioxide are considered in both simulation and experiment. Quality factors of over 104 are found via simulation, while quality factors of over 5×103 are found in experiment, for cavities with mode volumes of 2.0(λ/n)3 and in the visible wavelength range 600–716 nm. The dependences of the cavity quality factor and mode volume for different design parameters are also considered.
Vibron phonon in a lattice of H-bonded peptide units: A criterion to discriminate between the weak and the strong coupling limit
Authors: Pouthier Vincent
Published: January 2010

Based on dynamical considerations, a simple and intuitive criterion is established to measure the strength of the vibron-phonon coupling in a lattice of H-bonded peptide units. The main idea is to compare separately the influence of both the vibron-phonon coupling and the dipole-dipole interaction on a specific element of the vibron reduced density matrix. This element, which refers to the coherence between the ground state and a local excited amide-I mode, generalizes the concept of survival amplitude at finite temperature. On the one hand, when the dipole-dipole interaction is neglected, it is shown that dephasing-limited coherent dynamics is induced by the vibron-phonon coupling. On the other hand, when the vibron-phonon coupling is disregarded, decoherence occurs due to dipole-dipole interactions since the local excited state couples with neighboring local excited states. Therefore, our criterion simply states that the strongest interaction is responsible for the fastest decoherence. It yields a critical coupling χ∗≈25 pN at biological temperature.
A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks
Authors: Ramaswamy Rajesh , Sbalzarini Ivo F.
Published: January 2010

We present the partial-propensity stochastic simulation algorithm with composition-rejection sampling (PSSA-CR). It is an exact formulation of the stochastic simulation algorithm (SSA) for well-stirred systems of coupled chemical reactions. The new formulation is a partial-propensity variant [R. Ramaswamy, N. González-Segredo, and I. F. Sbalzarini, J. Chem. Phys. 130, 244104 (2009)] of the composition- rejection SSA [A. Slepoy, A. P. Thompson, and S. J. Plimpton, J. Chem. Phys. 128, 205101 (2008)]. The computational cost of this new formulation is bounded by a constant for weakly coupled reaction networks, and it increases at most linearly with the number of chemical species for strongly coupled reaction networks. PSSA-CR thus combines the advantages of partial-propensity methods and the composition-rejection SSA, providing favorable scaling of the computational cost for all classes of reaction networks.
Transition probabilities for the Au (S2, D2, and P2) with SiH4 reaction
Authors: Pacheco-Sánchez J. H. , Luna-García H. M. , García-Cruz L. M. , Novaro O.
Published: January 2010

Transition probabilities on the interaction of the ground and the lowest excited states of gold Au (S2:5d106s1, D2:5d96s2, and P2:5d106p1) with silane (SiH4) are studied through ab initio Hartree–Fock self-consistent field calculations, where the atom’s core is represented by relativistic effective core potentials. These calculations are followed by a multiconfigurational self-consistent field study. The correlation energy is accounted for through extensive variational and perturbative second order multireference Moller–Plesset configuration interaction analysis of selected perturbations obtained by iterative process calculations using the CIPSI program package. It is found that the Au atom in the (P2:5d106p1) state inserts in the Si–H bond. In this interaction its corresponding D A2′ potential energy surface is initially attractive and only becomes repulsive after encountering an avoided crossing with the initially repulsive C A2′ surface linked to the Au(D2:5d96s2)-SiH4 fragments. The A, B, and C A2′ curves derived from the Au(D2:5d96s2) atom interaction with silane are initially repulsive, each one of them showing two avoided crossings, while the A A2′ curve goes sharply downwards until it meets the X A2′ curve interacting adiabatically, which is linked with the Au(S2:5d106s1)-SiH4 moieties. The A A2′ curve becomes repulsive after the avoided crossing with the X A2′, curve. The lowest-lying X A2′ potential leads to the HAuSiH3 X A2′ intermediate molecule. This intermediate molecule, diabatically correlated with the Au(P2:5d106p1)+SiH4 system which lies 3.34 kcal/mol above the ground state reactants, has been carefully characterized as have the dissociation channels leading to the AuH+SiH3 and H+AuSiH3 products. These products are reached from the HAuSiH3 intermediate without any activation barrier. The Au–SiH4 calculation results are successfully compared to experiment. Landau–Zener theory of avoided crossings is applied to these interactions considering the angle θ instead of the distance r as the reaction coordinate.
Heat capacity of water: A signature of nuclear quantum effects
Authors: Vega C. , Conde M. M. , McBride C. , Abascal J. L. F. , Noya E. G. , Ramirez R. , Sesé L. M.
Published: January 2010

In this note we present results for the heat capacity at constant pressure for the TIP4PQ/2005 model, as obtained from path-integral simulations. The model does a rather good job of describing both the heat capacity of ice Ih and of liquid water. Classical simulations using the TIP4P/2005, TIP3P, TIP4P, TIP4P-Ew, simple point charge/extended, and TIP5P models are unable to reproduce the heat capacity of water. Given that classical simulations do not satisfy the third law of thermodynamics, one would expect such a failure at low temperatures. However, it seems that for water, nuclear quantum effects influence the heat capacities all the way up to room temperature. The failure of classical simulations to reproduce Cp points to the necessity of incorporating nuclear quantum effects to describe this property accurately.
Arabidopsis
synaptotagmin SYTA regulates endocytosis and virus movement protein cell-to-cell transport
Authors: Lewis Jennifer D. , Lazarowitz Sondra G.
Published: January 2010

Synaptotagmins are calcium sensors that regulate synaptic vesicle exo/endocytosis. Thought to be exclusive to animals, they have recently been characterized in plants. We show that
Arabidopsis
synaptotagmin SYTA regulates endosome recycling and movement protein (MP)-mediated trafficking of plant virus genomes through plasmodesmata. SYTA localizes to endosomes in plant cells and directly binds the distinct
Cabbage leaf curl virus
(CaLCuV) and
Tobacco mosaic virus
(TMV) cell-to-cell movement proteins. In a SYTA knockdown line, CaLCuV systemic infection is delayed, and cell-to-cell spread of TMV and CaLCuV movement proteins is inhibited. A dominant-negative SYTA mutant causes depletion of plasma membrane-derived endosomes, produces large intracellular vesicles attached to plasma membrane, and inhibits cell-to-cell trafficking of TMV and CaLCuV movement proteins, when tested in an
Agrobacterium
-based leaf expression assay. Our studies show that SYTA regulates endocytosis, and suggest that distinct virus movement proteins transport their cargos to plasmodesmata for cell-to-cell spread via an endocytic recycling pathway.
Transcriptional coactivator HCF-1 couples the histone chaperone Asf1b to HSV-1 DNA replication components
Authors: Peng Hua , Nogueira Mauricio L. , Vogel Jodi L. , Kristie Thomas M.
Published: January 2010

The cellular transcriptional coactivator HCF-1 interacts with numerous transcription factors as well as other coactivators and is a component of multiple chromatin modulation complexes. The protein is essential for the expression of the immediate early genes of both herpes simplex virus (HSV) and varicella zoster virus and functions, in part, by coupling chromatin modification components including the Set1 or MLL1 histone methyltransferases and the histone demethylase LSD1 to promote the installation of positive chromatin marks and the activation of viral immediately early gene transcription. Although studies have investigated the role of HCF-1 in both cellular and viral transcription, little is known about other processes that the protein may be involved in. Here we demonstrate that HCF-1 localizes to sites of HSV replication late in infection. HCF-1 interacts directly and simultaneously with both HSV DNA replication proteins and the cellular histone chaperone Asf1b, a protein that regulates the progression of cellular DNA replication forks via chromatin reorganization. Asf1b localizes with HCF-1 in viral replication foci and depletion of Asf1b results in significantly reduced viral DNA accumulation. The results support a model in which the transcriptional coactivator HCF-1 is a component of the HSV DNA replication assembly and promotes viral DNA replication by coupling Asf1b to DNA replication components. This coupling provides a novel function for HCF-1 and insights into the mechanisms of modulating chromatin during DNA replication.
The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules
Authors: Bouyain Samuel , Watkins Dara J.
Published: January 2010

The receptor protein tyrosine phosphatases gamma (PTPRG) and zeta (PTPRZ) are expressed primarily in the nervous system and mediate cell adhesion and signaling events during development. We report here the crystal structures of the carbonic anhydrase-like domains of PTPRZ and PTPRG and show that these domains interact directly with the second and third immunoglobulin repeats of the members of the contactin (CNTN) family of neural recognition molecules. Interestingly, these receptors exhibit distinct specificities: PTPRZ binds only to CNTN1, whereas PTPRG interacts with CNTN3, 4, 5, and 6. Furthermore, we present crystal structures of the four N-terminal immunoglobulin repeats of mouse CNTN4 both alone and in complex with the carbonic anhydrase-like domain of mouse PTPRG. In these structures, the N-terminal region of CNTN4 adopts a horseshoe-like conformation found also in CNTN2 and most likely in all CNTNs. This restrained conformation of the second and third immunoglobulin domains creates a binding site that is conserved among CNTN3, 4, 5, and 6. This site contacts a discrete region of PTPRG composed primarily of an extended β-hairpin loop found in both PTPRG and PTPRZ. Overall, these findings implicate PTPRG, PTPRZ and CNTNs as a group of receptors and ligands involved in the manifold recognition events that underlie the construction of neural networks.
Genetic contribution to individual variation in binocular rivalry rate
Authors: Miller Steven M. , Hansell Narelle K. , Ngo Trung T. , Liu Guang B. , Pettigrew John D. , Martin Nicholas G. , Wright Margaret J.
Published: January 2010

Binocular rivalry occurs when conflicting images are presented in corresponding locations of the two eyes. Perception alternates between the images at a rate that is relatively stable within individuals but that varies widely between individuals. The determinants of this variation are unknown. In addition, slow binocular rivalry has been demonstrated in bipolar disorder, a psychiatric condition with high heritability. The present study therefore examined whether there is a genetic contribution to individual variation in binocular rivalry rate. We employed the twin method and studied both monozygotic (MZ) twins (
n
= 128 pairs) who are genetically identical, and dizygotic (DZ) twins (
n
= 220 pairs) who share roughly half their genes. MZ and DZ twin correlations for binocular rivalry rate were 0.51 and 0.19, respectively. The best-fitting genetic model showed 52% of the variance in binocular rivalry rate was accounted for by additive genetic factors. In contrast, nonshared environmental influences accounted for 18% of the variance, with the remainder attributed to measurement error. This study therefore demonstrates a substantial genetic contribution to individual variation in binocular rivalry rate. The results support the vigorous pursuit of genetic and molecular studies of binocular rivalry and further characterization of slow binocular rivalry as an endophenotype for bipolar disorder.
Setdb2
restricts dorsal organizer territory and regulates left–right asymmetry through suppressing
fgf8
activity
Authors: Xu Peng-Fei , Zhu Kang-Yong , Jin Yi , Chen Yi , Sun Xiao-Jian , Deng Min , Chen Sai-Juan , Chen Zhu , Liu Ting Xi
Published: January 2010

Dorsal organizer formation is one of the most critical steps in early embryonic development. Several genes and signaling pathways that positively regulate the dorsal organizer development have been identified; however, little is known about the factor(s) that negatively regulates the organizer formation. Here, we show that Setdb2, a SET domain-containing protein possessing potential histone H3K9 methyltransferase activity, restricts dorsal organizer development and regulates left–right asymmetry by suppressing
fibroblast growth factor 8
(
fgf8
) expression. Knockdown of Setdb2 results in a massive expansion of dorsal organizer markers
floating head
(
flh
),
goosecoid
(
gsc
), and
chordin
(
chd
), as well as a significant increase of
fgf8
, but not
fgf4
mRNAs. Consequently, disrupted midline patterning and resultant randomization of left–right asymmetry are observed in Setdb2-deficient embryos. These characteristic changes induced by Setdb2 deficiency can be nearly corrected by either overexpression of a dominant-negative
fgf
receptor or knockdown of
fgf8
, suggesting an essential role for Setdb2–Fgf8 signaling in restricting dorsal organizer territory and regulating left–right asymmetry. These results provide unique evidence that a SET domain-containing protein potentially involved in the epigenetic control negatively regulates dorsal organizer formation during early embryonic development.
Analysis of the cellular mechanism underlying inhibition of EAE after treatment with anti-NKG2A F(ab′)
2
Authors: Leavenworth Jianmei W. , Schellack Carola , Kim Hye-Jung , Lu Linrong , Spee Pieter , Cantor Harvey
Published: January 2010

Autoimmune encephalomyelitis may be ameliorated experimentally by enhancing NK cell-mediated elimination of activated autoreactive T cells through a mutation that interrupts the interaction between Qa-1
b
and CD94/NKG2A. Here we evaluate the ability of an anti-NKG2A F(ab′)
2
Ab to enhance elimination of autoreactive T cells and reduce experimental autoimmune encephalomyelitis (EAE). Anti-NKG2A F(ab′)
2
treatment diminishes progression of both myelin oligodendrocyte glycoprotein (MOG)-induced EAE in intact C57BL/6 mice and after adoptive transfer of disease-causing T cells. Analyses of the underlying mechanism revealed that administration of anti-NKG2A F(ab′)
2
Ab reduces CD4
+
T recall responses to MOG and skews the proportion of IL-17- and IFNγ-producing CD4
+
T cells toward the protective IL-4- and IL-10-secreting CD4
+
T cell subpopulations. CD94/NKG2A-dependent inhibition of inflammatory damage to spinal cord is associated with decreased infiltration of T cells and reduced microglia activation in the central nervous system. Because anti-NKG2A F(ab′)
2
treatment had no detectable effect on the numbers or activity of T and B lymphocytes and NK cells in peripheral lymphoid tissues, this anti-NKG2A-based approach may represent a safe and effective therapy for this CNS disorder.
Synthetic design of strong promoters
Authors: Schlabach Michael R. , Hu Jimmy K. , Li Mamie , Elledge Stephen J.
Published: January 2010

We have taken a synthetic biology approach to the generation and screening of transcription factor binding sites for activity in human cells. All possible 10-mer DNA sequences were printed on microarrays as 100-mers containing 10 repeats of the same sequence in tandem, yielding an oligonucleotide library of 52,429 unique sequences. This library of potential enhancers was introduced into a retroviral vector and screened in multiple cell lines for the ability to activate GFP transcription from a minimal CMV promoter. With this method, we isolated 100 bp synthetic enhancer elements that were as potent at activating transcription as the WT CMV immediate early enhancer. The activity of the recovered elements was strongly dependent on the cell line in which they were recovered. None of the elements were capable of achieving the same levels of transcriptional enhancement across all tested cell lines as the CMV enhancer. A second screen, for enhancers capable of synergizing with the elements from the original screen, yielded compound enhancers that were capable of twofold greater enhancement activity than the CMV enhancer, with higher levels of activity than the original synthetic enhancer across multiple cell lines. These findings suggest that the 10-mer synthetic enhancer space is sufficiently rich to allow the creation of synthetic promoters of all strengths in most, if not all, cell types.
A gendered movement for liberation: Hamas’s women’s movement and nation building in contemporary Palestine
Authors: Younes Anna-Esther
Published: January 2010

This research on Hamas’s women’s movement explains the contemporary political and social involvement of women with a multilayered perspective of different theories based on a textual analysis of the movement’s publications (the Hamas Charta 1988 and the Electoral Program 2006, as well as women’s testimonies to popular media outlets). Subsequently, it is claimed that only a comprehensive combination of post-colonial studies, gender and nationalism studies can fully grasp women’s roles within the Hamas movement. Uniting these three approaches, there are three main hypotheses for women’s activism and role within Hamas. First, Hamas propagates gendered worldviews and roles within the nationalist project as well as within the movement. Those outlooks intersect with historized notions of Arab–Muslim identity as well as with notions of liberation against foreign (Western) occupation and colonialism. Second, the ‘women of Hamas’ use such gendered roles in order to pave the way for a pious, yet determined, women’s participation within the nationalist venture as well as the movement’s overall project of national liberation. Third, the gendered defence calculus springing from those views allows a restructuring of society in general, vis-à-vis the Palestinian population as well as vis-à-vis the Israeli-Palestinian conflict.
Resisting creeping urbanization and gentrification in the Old City of Jerusalem and its surroundings
Authors: Khamaisi Rassem
Published: January 2010

This paper (which is an excerpt from a book) examines the question of the revitalization of the Old City of Jerusalem as opposed to renovation or rehabilitation in connection with the question of the gentrification and Judaization of the ancient city through various measures. The author argues that demographic and geopolitical factors as well as Israeli policies have led to the deterioration of living conditions as well as living space in the Old City. An increase in population coupled with the changes effected by the border wall has meant that Palestinians have been forced to deal with increased need for living space in ways which are deemed extra-legal by Israeli authorities but which also work against preservation of the historic cultural integrity of the Old City of Jerusalem. The author argues that Palestinians should adopt strategies of ‘Forest Life’ and ‘Urban Village’, and that resistance as well as the role of the United Nations Educational, Scientific and Cultural Organization (UNESCO) should be utilized in what will improve Palestinian living conditions as well as preserve the cultural and historical integrity of the Old City of Jerusalem.
Force transmission in migrating cells
Authors: Fournier Maxime F. , Sauser Roger , Ambrosi Davide , Meister Jean-Jacques , Verkhovsky Alexander B.
Published: January 2010

During cell migration, forces generated by the actin cytoskeleton are transmitted through adhesion complexes to the substrate. To investigate the mechanism of force generation and transmission, we analyzed the relationship between actin network velocity and traction forces at the substrate in a model system of persistently migrating fish epidermal keratocytes. Front and lateral sides of the cell exhibited much stronger coupling between actin motion and traction forces than the trailing cell body. Further analysis of the traction–velocity relationship suggested that the force transmission mechanisms were different in different cell regions: at the front, traction was generated by a gripping of the actin network to the substrate, whereas at the sides and back, it was produced by the network’s slipping over the substrate. Treatment with inhibitors of the actin–myosin system demonstrated that the cell body translocation could be powered by either of the two different processes, actomyosin contraction or actin assembly, with the former associated with significantly larger traction forces than the latter.
Thin-film magneto-inductive cables
Authors: Syms R R A , Solymar L , Young I R , Floume T
Published: January 2010

Magneto-inductive cables for low (ca 100 MHz) radio frequencies are demonstrated in thin-film form. 20 cm long resonant elements are formed using double-sided patterning of copper-clad polyimide, based on single-turn inductors and parallel-plate capacitors that use the substrate as an interlayer dielectric. Continuous cables are formed by overlaying elements, in an arrangement that allows a high, positive coupling coefficient (κ > 0.6) to be achieved despite the use of a planar geometry. Equivalent circuit parameters are extracted from experiments on integrated coupling transducers, and propagation characteristics are compared with simple theory. Low propagation loss (4 dB m−1 at 55 MHz, falling to 2.3 dB m−1 at 130 MHz) is demonstrated near the operating frequencies of magnetic resonance imaging, for a potential application as patient-safe cable in internal imaging.
Measuring dislocation densities in nonpolar a-plane GaN films using atomic force microscopy
Authors: Moram M A , Johnston C F , Kappers M J , Humphreys C J
Published: January 2010

Dislocation densities in nonpolar GaN films were determined using atomic force microscopy (AFM) by counting pits in the GaN surface revealed by a SiH4 surface treatment. This treatment increased the number of pits detected by a factor of 2 compared with the untreated surface. AFM and transmission electron microscopy analysis of a series of SiH4-treated calibration samples indicated that surface pit and dislocation densities corresponded well up to a dislocation density of ∼6 × 109 cm−2, above which surface pit overlap meant that dislocation densities determined by AFM were underestimated. For all samples with dislocation densities below 6 × 109 cm−2, spatial analysis of the surface pit positions showed that dislocations typically accumulated in bands at island coalescence boundaries.
Wave propagation in a 2D sonic crystal with a Helmholtz resonant defect
Authors: Wu Liang-Yu , Chen Lien-Wen
Published: January 2010

In this paper, we study the wave propagation of a 2D local resonant sonic crystal consisting of polymethyl methacrylate cylinders in air background. The Helmholtz resonator is placed at the point defect to be a local resonant defect. Band structures are calculated by using the finite element method with a periodic boundary condition. Band structures of the sonic crystal with a circular and Helmholtz resonant (HR) defect are discussed and compared. The frequencies of the defect band depend strongly on the geometric size of the defect. The transmission spectra are measured experimentally. The experimental results are in good agreement with the analytical band structures. The defect mode characteristics of the sonic crystal with a HR defect can be used in the implementation of new acoustic devices.
A novel IS26 structure surrounds bla
CTX-M genes in different plasmids from German clinical Escherichia coli isolates
Authors: Cullik A. , Pfeifer Y. , Prager R. , von Baum H. , Witte W.
Published: January 2010

This report focuses on the molecular characterization of 22 extended-spectrum β-lactamase-producing Escherichia coli isolates collected in a German university hospital during a period of 9 months in 2006. Relationship analysis of clinical isolates was done via PFGE, multilocus sequence typing, plasmid profiling and additionally PCR for bla
ESBL detection and determination of phylogroups. After conjugal transfer, plasmid isolation and subsequent PCR for bla
ESBL detection and determination of incompatibility groups were performed. Using one-primer walking, up to 3600 bp upstream and downstream of different bla
CTX-M genes could be sequenced. β-Lactamases found were TEM-1 (n=14), SHV-5 (n=1) and a wide variety of CTX-M types (n=21), i.e. CTX-M-15 (n=12), CTX-M-1 (n=4), CTX-M-14 (n=2), CTX-M-9 (n=1), CTX-M-3 (n=1) and one new type, CTX-M-65 (n=1). In 18 isolates, bla
ESBL genes were located on conjugative plasmids of sizes between 40 and 180 kbp belonging to incompatibility groups FII (n=9), N (n=5) and I1 (n=4). bla
CTX-M was found to be associated with the common elements ISEcp1, IS26 and IS903-D, but with unusual spacer sequences for ISEcp1 in two isolates. These insertion sequences, connected to bla
CTX-M as well as other genes, were located between two IS26 elements in a configuration that has not yet been described. The results reveal the emergence of bla
ESBL, predominantly bla
CTX-M, located on different plasmids harboured by genotypically different E. coli strains. The identical gene arrangement in the bla
CTX-M neighbourhood in plasmids of different incompatibility groups indicates a main role of IS26 in distribution of mobile resistance elements between different plasmids.
In vitro postantibiotic effects of tomopenem (CS-023)against Staphylococcus aureus and Pseudomonas aeruginosa
Authors: Tomozawa Takanori , Sugihara Chika , Kakuta Masayo , Sugihara Kiyoshi , Koga Tetsufumi
Published: January 2010

The postantibiotic effect (PAE) of tomopenem was determined aftera 2 h exposure of two strains of meticillin-susceptible and meticillin-resistant Staphylococcus aureus (MSSA and MRSA), and imipenem-susceptibleand imipenem-resistant Pseudomonas aeruginosa, to tenfold the respectiveMIC. The PAEs on MSSA and P. aeruginosa were approximately 1 hand they were comparable to those of meropenem. The PAE on MRSA was 1.5 to3 h, equal to or longer than those of vancomycin. The PAEs of tomopenemnot only were found for MRSA, but also were present in the imipenem-resistant P. aeruginosa tested.
Influence of RpoN on isocitrate lyase activity in Pseudomonas aeruginosa
Authors: Hagins Jessica M. , Scoffield Jessica A. , Suh Sang-Jin , Silo-Suh Laura
Published: January 2010

Pseudomonas aeruginosa is the major aetiological agent of chronic pulmonary infections in patients with cystic fibrosis (CF). The metabolic pathways utilized by P. aeruginosa during these infections, which can persist for decades, are poorly understood. Several lines of evidence suggest that the glyoxylate pathway, which utilizes acetate or fatty acids to replenish intermediates of the tricarboxylic acid cycle, is an important metabolic pathway for P. aeruginosa adapted to the CF lung. Isocitrate lyase (ICL) is one of two major enzymes of the glyoxylate pathway. In a previous study, we determined that P. aeruginosa is dependent upon aceA, which encodes ICL, to cause disease on alfalfa seedlings and in rat lungs. Expression of aceA in PAO1, a P. aeruginosa isolate associated with acute infection, is regulated by carbon sources that utilize the glyoxyate pathway. In contrast, expression of aceA in FRD1, a CF isolate, is constitutively upregulated. Moreover, this deregulation of aceA occurs in other P. aeruginosa isolates associated with chronic infection, suggesting that high ICL activity facilitates adaptation of P. aeruginosa to the CF lung. Complementation of FRD1 with a PAO1 clone bank identified that rpoN negatively regulates aceA. However, the deregulation of aceA in FRD1 was not due to a knockout mutation of rpoN. Regulation of the glyoxylate pathway by RpoN is likely to be indirect, and represents a unique regulatory role for this sigma factor in bacterial metabolism.
Analysis of HmsH and its role in plague biofilm formation
Authors: Abu Khweek Arwa , Fetherston Jacqueline D. , Perry Robert D.
Published: January 2010

TheYersinia pestisHms+phenotype is a manifestation of biofilm formation that causes adsorption of Congo red and haemin at 26 °C but not at 37 °C. This phenotype is required for blockage of the proventricular valve of the oriental rat flea and plays a role in transmission of bubonic plague from fleas to mammals. Genes responsible for this phenotype are located in three separate operons,hmsHFRS,hmsTandhmsP.HmsH and HmsF are outer membrane (OM) proteins, while the other four Hms proteins are located in the inner membrane. According to the Hidden Markov Method-based predictor, HmsH has a large N terminus in the periplasm, aβ-barrel structure with 16β-strands that traverse the OM, eight surface-exposed loops, and seven short turns connecting theβ-strands on the periplasmic side. Here, we demonstrate that HmsH is a heat-modifiable protein, a characteristic of otherβ-barrel proteins, thereby supporting the bioinformatics analysis. Alanine scanning mutagenesis was used to identify conserved amino acids in the HmsH-like family that are critical for the function of HmsH in biofilm formation. Of 23 conserved amino acids mutated, four residues affected HmsH function and three likely caused protein instability. We used formaldehyde cross-linking to demonstrate that HmsH interacts with HmsF but not with HmsR, HmsS, HmsT or HmsP. Loss-of-function HmsH variants with single alanine substitutions retained theirβ-structure and interaction with HmsF. Finally, using a polarhmsH : : mini-kanmutant, we demonstrated that biofilm development is not important for the pathogenesis of bubonic or pneumonic plague in mice.
Structures of dipeptides: the head-to-tail story
Authors: Görbitz Carl Henrik
Published: January 2010

The hydrogen-bonding patterns in crystal structures of unprotected, zwitterionic dipeptides are dominated by head-to-tail chains involving the N-terminal amino groups and the C-terminal carboxylate groups. Patterns that include two concomitant chains, thus generating a hydrogen-bonded layer, are of special interest. A comprehensive survey shows that dipeptide structures can conveniently be divided into only four distinct patterns, differing by definition in the symmetry of the head-to-tail chains and amide hydrogen-bonding type, but also in other properties such as peptide conformation and the propensity to include solvent water or various organic guest molecules. Upon crystallization, the choice of pattern for a specific dipeptide is not random, but follows from the amino acid sequence.
Structures of incommensurate and commensurate composite crystals RbxMnO2(x= 1.3711, 1.3636)
Authors: Nuss Jürgen , Pfeiffer Steffen , van Smaalen Sander , Jansen Martin
Published: January 2010

Rb1.3711MnO2(Rb11Mn8O16) has been synthesizedviathe azide/nitrate route from a stoichiometric mixture of the precursors Mn2O3, RbNO3and RbN3. The structure of this extremely air- and moisture-sensitive compound can best be described in terms of an incommensurate composite structure, built up by a honeycomb-like framework of Rb ions, as one subsystem and by a second subsystem of chains, consisting of edge-sharing MnO4/2tetrahedra. These two composite substructures interpenetrate in such a way that the manganate chain polyanions centre the channels of the Rb-honeycomb framework. Crystals transform by an aging process into Rb1.3636MnO2(Rb15Mn11O22), which has a similar structure but a different commensurate modulation. Two reasons can be established for the origin of the modulations: the charge ordering of Mn2+/Mn3+on one hand, and the incompatibility of the Mn—Mn and Rb—Rb separations on the other.
Evaluation and analysis of criteria and sub‐criteria of a construction excellence model
Authors: Bassioni H.A. , Hassan T.M. , Price A.D.F.
Published: January 2010

Purpose

The purpose of this paper is to evaluate and analyse the criteria and sub‐criteria of an excellence model for construction that would aid construction contractors in measuring and improving their business performance.

Design/methodology/approach

The methodology of evaluation was based on similar evaluations of total quality management frameworks and excellence models in the literature. The developed model was measured via a questionnaire survey. The questionnaire as a measuring instrument was evaluated in terms of reliability and validity using techniques such as factor analysis, multiple correlation, and Cronbach's alpha. The weights of the criteria were empirically calculated using factor regression coefficients.

Findings

The criteria and sub‐criteria of the proposed construction excellence model were confirmed using empirical data, and the criterion weights were suggested on an empirical / scientific basis.

Research limitations/implications

The model is limited as a managerial tool: it can increase the chances of success, but not guarantee it. The model was evaluated on, and therefore limited to, large construction contracting organisations.

Originality/value

The main benefit of the construction excellence model is that it provides criteria and sub‐criteria for an excellence model developed for and evaluated by construction companies. It has a more comprehensive and wider coverage of performance criteria relevant to the construction industry than other excellence models.
The selection of sharing ratios in target cost contracts
Authors: Badenfelt Ulrika
Published: January 2010

Purpose

The purpose of this paper is to provide a broader understanding of target cost arrangements by empirical study of the choice of sharing ratios from the perspective of both clients and contractors.

Design/methodology/approach

Eight Swedish construction clients and eight contractors were interviewed. These interviews were followed by a case study of a large construction project with a target cost contract. The data for the case study were gathered through interviews, contract documents and non‐participant observation. The impact of perceived risks on the selection process is discussed in terms of agency theory.

Findings

Key factors influencing the selection of a sharing ratio included perceptions of fairness, knowledge of target cost contracts, and long‐term relationships. The perceived level of risk is affected by the perceived performance risk and the perceived relational risk. Consequently, attention should be paid to the impact of long‐term relationships on the design and outcome of target cost contracts since such relationships reduce the risks associated with asymmetric information, such as relational risk.

Originality/value

This study identifies factors that previous research has ignored in relation to the negotiation of target cost contracts.