bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal evolution of wake behind a rotationally oscillating circular cylinder
Authors: Lee Sang-Joon , Lee Jung-Yeop
Published: October 2007

The temporal evolution of the near-wake behind a circular cylinder undergoing rotational oscillatory motion with a relatively high forcing frequency has been investigated experimentally using a dynamic particle image velocimetry velocity field measurement technique. Experiments were carried out varying the frequency ratio FR (=ff∕fn), the ratio of the forcing frequency ff to the natural vortex shedding frequency fn, in the range of 0.0 (stationary) to 1.0 at an oscillation amplitude of θA=30° and Reynolds number of Re=4.14×103. Depending on the forcing condition (FR), the near-wake flow showed markedly different flow regimes: stationary (FR=0.0), non-lock-on (FR=0.4) and lock-on (FR=1.0) regimes. However, at all the frequency ratios tested, the power spectral density distributions showed a single dominant peak at the same vortex shedding frequency. As the forcing frequency was increased, the rotational oscillatory motion of the cylinder decreased the length of the vortex formation region and enhanced the mutual interaction between large-scale vortices across the wake centerline. In particular, the entrainment of ambient fluid seemed to play an important role in controlling the near-wake flow and shear-layer instability. The shear-layer instability showed different mechanisms compared with the case of small oscillation amplitude. A strong vortex motion appeared in the near-wake region. In addition, the rotational oscillatory motion of the cylinder changed the local mean flow structure significantly; thereby mean velocity profiles for each frequency ratio varied markedly in the vortex formation region. The configuration of vorticity contours shrunk toward the cylinder as the frequency ratio was increased. The temporally resolved flow information extracted in the present work is useful for understanding the evolution of vortex structure and analyzing the effects of open-loop active flow control technique on the near-wake flow structure.
Asymmetric band profile of the Soret band of deoxymyoglobin is caused by electronic and vibronic perturbations of the heme group rather than by a doming deformation
Authors: Schweitzer-Stenner Reinhard , Gorden John Paul , Hagarman Andrew
Published: October 2007

We measured the Soret band of deoxymyoglobin (deoxyMb), myoglobin cyanide (MbCN), and aquo-metmyoglobin (all from horse heart) with absorption and circular dichroism (CD) spectroscopies. A clear non-coincidence was observed between the absorption and CD profiles of deoxyMb and MbCN, with the CD profiles red- and blueshifted with respect to the absorption band position, respectively. On the contrary, the CD and absorption profiles of aquametMb were nearly identical. The observed noncoincidence indicates a splitting of the excited B state due to heme-protein interactions. CD and absorption profiles of deoxyMb and MbCN were self-consistently analyzed by employing a perturbation approach for weak vibronic coupling as well as the relative intensities and depolarization ratios of seven bands in the respective resonance Raman spectra measured with B-band excitation. The respective By component was found to dominate the observed Cotton effect of both myoglobin derivatives. The different signs of the noncoincidences between CD and absorption bands observed for deoxyMb and MbCN are due to different signs of the respective matrix elements of A1g electronic interstate coupling, which reflects an imbalance of Gouterman’s 50:50 states. The splitting of the B band reflects contributions from electronic and vibronic perturbations of B1g symmetry. The results of our analysis suggest that the broad and asymmetric absorption band of deoxyMb results from this band splitting rather than from its dependence on heme doming. Thus, we are able to explain recent findings that the temperature dependences of CO rebinding to myoglobin and the Soret band profile are uncorrelated[Ormos et al., Proc. Natl. Acad. Sci U.S.A. 95, 6762 (1998)].
Demonstration of magnetoelectric scanning probe microscopy
Authors: Hattrick-Simpers Jason R. , Dai Liyang , Wuttig Manfred , Takeuchi Ichiro , Quandt Eckhard
Published: October 2007

A near-field room temperature scanning magnetic probe microscope has been developed using a laminated magnetoelectric sensor. The simple trilayer longitudinal-transverse mode sensor, fabricated using Metglas as the magnetostrictive layer and polyvinylidene fluoride as the piezoelectric layer, shows an ac field sensitivity of 467±3μV∕Oe in the measured frequency range of 200Hz–8kHz. The microscope was used to image a 2mm diameter ring carrying an ac current as low as 10−5A. ac fields as small as 3×10−10T have been detected.
Control of concerted two bond versus single bond dissociation in CH3Co(CO)4 via an intermediate state using pump-dump laser pulses
Authors: Ambrosek David , González Leticia
Published: October 2007

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH3Co(CO)4 indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH3 and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.
Observation of atmospheric pressure arc on a cold cathode
Authors: Rao Lakshminarayana , Munz Richard J. , Coulombe Sylvain
Published: October 2007

Pictures of an atmospheric pressure arc between two concentric copper electrodes at different external magnetic fields (B field) were taken using a charge-coupled device camera and a complementary metal-oxide-semiconductor camera. The pictures reveal splitting of the arc column into a column with multiple arc roots (i.e., cathode spots), repulsion of cathode spots due to their self-induced B fields, and grouping of cathode spots under the influence of B field. Power frequency spectra analysis of the voltage fluctuations was also performed.
Assessment of transition operator reference states in electron propagator calculations
Authors: Flores-Moreno Roberto , Zakrzewski V. G. , Ortiz J. V.
Published: October 2007

The transition operator method combined with second-order, self-energy corrections to the electron propagator (TOEP2) may be used to calculate valence and core-electron binding energies. This method is tested on a set of molecules to assess its predictive quality. For valence ionization energies, well known methods that include third-order terms achieve somewhat higher accuracy, but only with much higher demands for memory and arithmetic operations. Therefore, we propose the use of the TOEP2 method for the calculation of valence electron binding energies in large molecules where third-order methods are infeasible. For core-electron binding energies, TOEP2 results exhibit superior accuracy and efficiency and are relatively insensitive to the fractional occupation numbers that are assigned to the transition orbital.
Investigation of the emitter band gap widening of heterojunction solar cells by use of hydrogenated amorphous carbon silicon alloys
Authors: Mueller T. , Duengen W. , Ma Y. , Job R. , Scherff M. , Fahrner W. R.
Published: October 2007

The hydrogenated amorphous carbon-silicon alloys [a-SixC1−x(n):Hy] and [a-Six(n):Hy] layers were investigated in order to prove the feasibility to widen the optical band gap in emitters of the heterojunction solar cells. The alloys were fabricated by decomposition of silane (SiH4), phosphine (PH3), methane (CH4), and hydrogen (H2), using a plasma enhanced chemical vapor deposition. Particularly, we focused on the incorporation of hydrogen and carbon within the resulting [a-SixC1−x(n):Hy] and [a-Six(n):Hy] films, which later form the emitter. The corresponding local vibrational modes of Si−Hx, C−H, and the corresponding network have been analyzed by μ-Raman spectroscopy. The addition of carbon degrades the photoelectronic properties in the emitter layer. This deterioration can be minimized by H dilution. The resulting optical band gap EG as well as the thickness of the emitter were determined by spectroscopic ellipsometry. It was confirmed that the band gap EG can be tailored by using an appropriate gas mixture during the decomposition. Furthermore, we analyzed the I−V characteristics of the prepared heterojunction solar cells. A trade-off between the electrical defects density and the optical losses induced an improvement of the I−V characteristics with increasing carbon and hydrogen concentration in the feedstock during the deposition.
In-fiber colloidal photonic crystals and the formed stop band in fiber longitudinal direction
Authors: Lin Yuankun , Herman Peter R. , Xu Wei
Published: October 2007

We report a microfluid-guided growth of colloidal photonic crystals inside a twin-hole optical fiber. The microfluid is pumped by the vapor pressure and capillary force of the solvent sealed in a vial. A face-centered-cubic lattice-type structure has been achieved for colloidal photonic crystals grown inside the twin-hole optical fiber. The colloidal crystal growths at air-colloid interfaces, fiber microchannel-colloid interfaces, and crystal-colloid boundaries are studied with scanning electronic microscope. Optical reflection measurement reveals a stop band along the fiber longitudinal direction due to the Bragg diffraction of in-fiber colloidal photonic crystals. The in-fiber photonic crystal adds an optical function to the microstructure optical fiber by incorporating spectral control through a structural resonance in the cladding region of the optical fiber.
Molecular dynamics simulations of signal transmission through a glycine peptide chain
Authors: Miao Ling , Seminario Jorge M.
Published: October 2007

The injection of finite duration vibrational signals encoding information into a biomolecular wire of the polypeptide glycine1000 is investigated theoretically using molecular dynamics simulations and digital signal processing techniques. We demonstrate that the amplitude modulated signal applied to one of the C–N bonds of the molecule transmits in the two directions through the long polypeptide molecule, which is connected to gold clusters at each of its ends. A decay of the signal propagation speed is observed along with intensity decay. On the other hand, the molecular dynamics simulations show that signal transmission is completely achievable at room temperature, thus realistic transmission of signals through linear molecules can be performed.
Spatiotemporal behavior of excited Xe*(1s4,1s5) and Kr*(1s5) atoms measured by laser-absorption spectroscopy in unit cell of a plasma display panel with Xe–Kr–Ne ternary gas mixture
Authors: Oh Jun-Seok , Tachibana Kunihide
Published: October 2007

We have studied the effects of ternary gas mixtures of Xe(10%)–Kr(20% and 40%)–Ne on the luminous efficiency in ac plasma display panels. Spatiotemporal behaviors of near infrared (IR) emission was measured by an intensified charge-coupled device camera equipped with a narrow bandpass filter and absolute densities of excited Xe* and Kr* atoms in the lowest resonance (1s4) and metastable (1s5) levels were measured by a technique of microscopic laser absorption spectroscopy. We have found interesting features from both emission and absorption experiments, such as longer near-IR emission (0.3–0.4μs) and different temporal behaviors between the excited Kr*(1s5) atoms and Xe*(1s4,1s5) atoms. We have also found that the order of magnitude of the peak density of excited Kr*(1s5) atoms (∼1012cm−3) was ten times smaller than that of Xe*(1s4,1s5) atoms, and that their decay time was remarkably short (∼0.3μs). These results have then been compared with those for a binary gas mixture of Xe(10%)–Ne. At a certain range of the sustain voltage, the production rate of Xe*(1s4,1s5) atoms and the luminous efficiency have turned out to be slightly improved for the ternary gas mixtures, compared to the binary gas mixture.
Femtosecond carrier dynamics of InxGa1−xN thin films grown on GaN (0001): Effect of carrier-defect scattering
Authors: Lioudakis Emmanouil , Othonos Andreas , Iliopoulos Eleftherios , Tsagaraki Katerina , Georgakilas Alexandros
Published: October 2007

Ultrafast carrier dynamics in ultrathin InxGa1−xN ternary alloys were investigated in detail, using femtosecond transient differential optical absorption measurements. Measurements were performed with probing wavelengths above and below the band edge of the materials. Furthermore, we performed a structural characterization by x-ray diffraction reciprocal space maps and we found that the alloys with the higher InN mole fraction (x=0.89 and x=0.43) present large lattice mismatch-strain relaxation whereas the lower InN content alloy was fully coherent with the underlying GaN (0001) layer. Our analysis showed that the observed nonradiative carrier dynamics was strongly related with the carrier-defect scattering of the materials. Our measurements in conjunction with the numerical analysis showed that when we excite these alloys with ultrashort laser pulses the background carrier concentration for In-rich InGaN samples participates to the photoexcited carrier relaxation process via carrier momentum scattering. For the higher InN content alloys (x=0.89 and 0.43) the relaxation times were short (0.4–1.4ps) whereas for the full strained alloy (x=0.07) a slower nonradiative relaxation time (∼25ps) was observed. Finally, the energy loss rate of this material (2.05±0.10meV∕fs) as well as the optical phonon lifetime (44±2fs) were extracted.
Two-photon excitation studies in terbium doped yttrium aluminum oxide
Authors: Kommidi Praveena , Reddy B. Rami
Published: October 2007

Two-photon excitation studies were performed in YAlO3:Tb3+. Under 488nm excitation fluorescence emission occurred from the D45 to the Fj7 levels. In addition, violet emission also occurred from D35 to Fj7 levels. Ground and excited state absorption coefficients were derived by fitting the transmission data to a nonlinear equation. When the sample was excited with 488 and 796nm simultaneously, violet emission intensity increased significantly. Excited state excitation spectra were also recorded.
A narrow-band injection-seeded pulsed titanium:sapphire oscillator-amplifier system with on-line chirp analysis for high-resolution spectroscopy
Authors: Hannemann S. , van Duijn E.-J. , Ubachs W.
Published: October 2007

A narrow-band tunable injection-seeded pulsed titanium:sapphire laser system has been developed for application in high-resolution spectroscopic studies at the fundamental wavelengths in the near infrared as well as in the ultraviolet, deep ultraviolet, and extreme ultraviolet after upconversion. Special focus is on the quantitative assessment of the frequency characteristics of the oscillator-amplifier system on a pulse-to-pulse basis. Frequency offsets between continuous-wave seed light and the pulsed output are measured as well as linear chirps attributed mainly to mode pulling effects in the oscillator cavity. Operational conditions of the laser are found in which these offset and chirp effects are minimal. Absolute frequency calibration at the megahertz level of accuracy is demonstrated on various atomic and molecular resonance lines.
Schottky contact on a ZnO (0001) single crystal with conducting polymer
Authors: Nakano M. , Tsukazaki A. , Gunji R. Y. , Ueno K. , Ohtomo A. , Fukumura T. , Kawasaki M.
Published: October 2007

High quality Schottky junctions were fabricated on a ZnO (0001) bulk single crystal by spin coating a commercial conducting polymer, poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS), as the metal electrodes. The junctions exhibited excellent rectifying behavior with a typical ideality factor of 1.2. Such parameters as Schottky barrier height (ϕb) and built-in potential (Vbi) show negligible variation among junctions. The electron affinity of ZnO derived from ϕb and qVbi values show a slight deviation (∼0.2eV), suggesting the existence of spontaneously formed interfacial dipole layer between ZnO (0001) polar surface and anionic PSS molecules.
Hysteretic transfer characteristics of double-walled and single-walled carbon nanotube field-effect transistors
Authors: Yuan Shaoning , Zhang Qing , Shimamoto Daisuke , Muramatsu Hiroyuki , Hayashi Takuya , Kim Yoong Ahm , Endo Morinobu
Published: October 2007

In both double-walled carbon nanotube field-effect transistors (DWCNT-FETs) and single-walled carbon nanotube field-effect transistors (SWCNT-FETs), “clockwise” hysteretic transfer characteristics are observed. These characteristics can be attributed to mobile ions or charged clusters in surfactant layers around the tube channels. Compared with SWCNT-FETs, more significant surfactant influences on the transfer characteristics are observed in DWCNT-FETs due to superior surfactant adsorption properties of double-walled carbon nanotubes. Our findings suggest that not only water molecules but also the surfactants play critical roles in dominating the hystereses, especially when the carbon nanotubes are double walled.
Dielectric and piezoelectric properties of (K0.5Na0.5)NbO3–Ba(Zr0.05Ti0.95)O3 lead-free ceramics
Authors: Lin Dunmin , Kwok K. W. , Chan H. W. L.
Published: October 2007

Lead-free ceramics (1−x)(K0.5Na0.5)NbO3–xBa(Zr0.05Ti0.95)O3 doped with 1mol% MnO2 have been fabricated by pressureless sintering. With the MnO2 doping, all the ceramics can be well sintered at 1100–1160°C and exhibit a dense and pure perovskite structure. After the addition of Ba(Zr0.05Ti0.95)O3, a relax behavior is induced and both the cubic-tetragonal and tetragonal-orthorhombic phase transitions shift to lower temperatures. Coexistence of the orthorhombic and tetragonal phases is hence formed in the ceramics with 0.04<x<0.07 at room temperature. It is suggested that owing to the more possible polarization states resulting from the coexistence of the two phases, the piezoelectric and dielectric properties of the ceramics are enhanced significantly. The ceramic with x=0.06 exhibits the following optimum properties: d33=234pC∕N, kp=0.49, kt=0.48, εr=1191, tanδ=1.20%, and TC=318°C.
A silicon-based spot-size converter between single-mode fibers and Si-wire waveguides using cascaded tapers
Authors: Shiraishi Kazuo , Yoda Hidehiko , Ohshima Akihiko , Ikedo Hideki , Tsai Chen S.
Published: October 2007

Theoretical and experimental performances of a robust Si-based spot-size converter (SSC) for efficient coupling between a single-mode fiber and a photonic Si-wire waveguide are reported. The SSC is comprised of cascaded horizontal linear and vertical nonlinear up tapers measured 2.0mm and 86μm in length, respectively, in a silicon-on-insulator substrate. The fine modal field of a Si-wire waveguide, 0.54×0.38μm2 in diameters, was expanded to diameters of 5.1×9.2μm2 with measured net transmission loss of 0.5dB at the wavelength of 1.55μm by the miniature SSC.
Voltage-controlled variable light emissions from GaN codoped with Eu, Er, and Tm
Authors: Zhang L. , Liu F. Q. , Liu C.
Published: October 2007

In this letter, a model to calculate the emission intensities of different rare-earth (RE) dopants in GaN is proposed based on the quantum collision theory and Judd-Ofelt approximation. The possible white light emission from Eu-, Er-, and Tm-codoped GaN is predicted according to the Commission International de I’Eclairage chromaticity diagram. Variable-wavelength emissions can be realized by adjusting the relative concentrations of different RE dopants in GaN and the bias voltage of the applied electric field. The availability of voltage-controlled light emissions and white light emission of the RE-doped GaN electroluminescent devices may have great potential for application in displays.
Critical behavior in Ti-doped manganites LaMn1−xTixO3 (0.05⩽x⩽0.2)
Authors: Yang J. , Lee Y. P.
Published: October 2007

The critical properties of the ferromagnetic insulating system LaMn1−xTixO3 (0.05⩽x⩽0.2) are investigated based on the static magnetization measurements around Curie temperature TC. The values of critical exponents, derived from the magnetic data using the Kouvel-Fisher method, yield 0.359⩽β⩽0.378, 1.24⩽γ⩽1.29, and 4.11⩽δ⩽4.21 with a TC of 95–173K. The exponent values are close to those expected for three-dimensional Heisenberg ferromagnets with short-range interactions, and the magnetic transition is understood in the context of Griffiths phase, arising from the random-temperature effects.
Sustainable vector control and management of Chagas disease in the Gran Chaco, Argentina
Authors: Gürtler Ricardo E. , Kitron Uriel , Cecere M. Carla , Segura Elsa L. , Cohen Joel E.
Published: October 2007

Chagas disease remains a serious obstacle to health and economic development in Latin America, especially for the rural poor. We report the long-term effects of interventions in rural villages in northern Argentina during 1984–2006. Two community-wide campaigns of residual insecticide spraying immediately and strongly reduced domestic infestation and infection with
Trypanosoma cruzi
in
Triatoma infestans
bugs and dogs and more gradually reduced the seroprevalence of children <15 years of age. Because no effective surveillance and control actions followed the first campaign in 1985, transmission resurged in 2–3 years. Renewed interventions in 1992 followed by sustained, supervised, community-based vector control largely suppressed the reestablishment of domestic bug colonies and finally led to the interruption of local human
T. cruzi
transmission. Human incidence of infection was nearly an order of magnitude higher in peripheral rural areas under pulsed, unsupervised, community-based interventions, where human transmission became apparent in 2000. The sustained, supervised, community-based strategy nearly interrupted domestic transmission to dogs but did not eliminate
T. infestans
despite the absence of pyrethroid-insecticide resistance.
T. infestans
persisted in part because of the lack of major changes in housing construction and quality. Sustained community participation grew out of establishing a trusted relationship with the affected communities and the local schools. The process included health promotion and community mobilization, motivation, and supervision in close cooperation with locally nominated leaders.
Anorexia induced by activation of serotonin 5-HT4receptors is mediated by increases in CART in the nucleus accumbens
Authors: Jean Alexandra , Conductier Grégory , Manrique Christine , Bouras Constantin , Berta Philippe , Hen René , Charnay Yves , Bockaert Joël , Compan Valérie
Published: October 2007

Anorexia nervosa is a growing concern in mental health, often inducing death. The potential neuronal deficits that may underlie abnormal inhibitions of food intake, however, remain largely unexplored. We hypothesized that anorexia may involve altered signaling events within the nucleus accumbens (NAc), a brain structure involved in reward. We show here that direct stimulation of serotonin (5-hydroxytryptamine, 5-HT) 4 receptors (5-HT4R) in the NAc reduces the physiological drive to eat and increases CART (cocaine- and amphetamine-regulated transcript) mRNA levels in fed and food-deprived mice. It further shows that injecting 5-HT4R antagonist or siRNA-mediated 5-HT4R knockdown into the NAc induced hyperphagia only in fed mice. This hyperphagia was not associated with changes in CART mRNA expression in the NAc in fed and food-deprived mice. Results include that 5-HT4R control CART mRNA expression into the NAc via a cAMP/PKA signaling pathway. Considering that CART may interfere with food- and drug-related rewards, we tested whether the appetite suppressant properties of 3,4-N-methylenedioxymethamphetamine (MDMA, ecstasy) involve the 5-HT4R. Using 5-HT4R knockout mice, we demonstrate that 5-HT4R are required for the anorectic effect of MDMA as well as for the MDMA-induced enhancement of CART mRNA expression in the NAc. Directly injecting CART peptide or CART siRNA into the NAc reduces or increases food consumption, respectively. Finally, stimulating 5-HT4R- and MDMA-induced anorexia were both reduced by injecting CART siRNA into the NAc. Collectively, these results demonstrate that 5-HT4R-mediated up-regulation of CART in the NAc triggers the appetite-suppressant effects of ecstasy.
Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks
Authors: Behar Marcelo , Dohlman Henrik G. , Elston Timothy C.
Published: October 2007

Intracellular signaling pathways that share common components often elicit distinct physiological responses. In most cases, the biochemical mechanisms responsible for this signal specificity remain poorly understood. Protein scaffolds and cross-inhibition have been proposed as strategies to prevent unwanted cross-talk. Here, we report a mechanism for signal specificity termed “kinetic insulation.” In this approach signals are selectively transmitted through the appropriate pathway based on their temporal profile. In particular, we demonstrate how pathway architectures downstream of a common component can be designed to efficiently separate transient signals from signals that increase slowly over time. Furthermore, we demonstrate that upstream signaling proteins can generate the appropriate input to the common pathway component regardless of the temporal profile of the external stimulus. Our results suggest that multilevel signaling cascades may have evolved to modulate the temporal profile of pathway activity so that stimulus information can be efficiently encoded and transmitted while ensuring signal specificity.
Protein stability imposes limits on organism complexity and speed of molecular evolution
Authors: Zeldovich Konstantin B. , Chen Peiqiu , Shakhnovich Eugene I.
Published: October 2007

Classical population genetics
a priori
assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from physical properties of proteins under a physiological assumption that loss of stability of any protein encoded by an essential gene confers a lethal phenotype. Accumulation of mutations in organisms containing Γ genes can then be represented as diffusion within the Γ-dimensional hypercube with adsorbing boundaries determined, in each dimension, by loss of a protein's stability and, at higher stability, by lack of protein sequences. Solving the diffusion equation whose parameters are derived from the data on point mutations in proteins, we determine a universal distribution of protein stabilities, in agreement with existing data. The theory provides a fundamental relation between mutation rate, maximal genome size, and thermodynamic response of proteins to point mutations. It establishes a universal speed limit on rate of molecular evolution by predicting that populations go extinct (via lethal mutagenesis) when mutation rate exceeds approximately six mutations per essential part of genome per replication for mesophilic organisms and one to two mutations per genome per replication for thermophilic ones. Several RNA viruses function close to the evolutionary speed limit, whereas error correction mechanisms used by DNA viruses and nonmutant strains of bacteria featuring various genome lengths and mutation rates have brought these organisms universally ≈1,000-fold below the natural speed limit.
Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells
Authors: Roach Jared C. , Smith Kelly D. , Strobe Katie L. , Nissen Stephanie M. , Haudenschild Christian D. , Zhou Daixing , Vasicek Thomas J. , Held G. A. , Stolovitzky Gustavo A. , Hood Leroy E. , Aderem Alan
Published: October 2007

Transcription factors play a key role in integrating and modulating biological information. In this study, we comprehensively measured the changing abundances of mRNAs over a time course of activation of human peripheral-blood-derived mononuclear cells (“macrophages”) with lipopolysaccharide. Global and dynamic analysis of transcription factors in response to a physiological stimulus has yet to be achieved in a human system, and our efforts significantly advanced this goal. We used multiple global high-throughput technologies for measuring mRNA levels, including massively parallel signature sequencing and GeneChip microarrays. We identified 92 of 1,288 known human transcription factors as having significantly measurable changes during our 24-h time course. At least 42 of these changes were previously unidentified in this system. Our data demonstrate that some transcription factors operate in a functional range below 10 transcripts per cell, whereas others operate in a range three orders of magnitude greater. The highly reproducible response of many mRNAs indicates feedback control. A broad range of activation kinetics was observed; thus, combinatorial regulation by small subsets of transcription factors would permit almost any timing input to
cis
-regulatory elements controlling gene transcription.
Sticky overhangs enhance siRNA-mediated gene silencing
Authors: Bolcato-Bellemin Anne-Laure , Bonnet Marie-Elise , Creusat Gaëlle , Erbacher Patrick , Behr Jean-Paul
Published: October 2007

siRNA delivery to cells offers a convenient and powerful means of gene silencing that bypasses several barriers met by gene delivery. However, nonviral vectors, and especially polymers, form looser complexes with siRNA than with plasmid DNA. As a consequence, exchange of siRNA for larger polymeric anions such as proteoglycans found outside cells and at their surface may occur and lower delivery. We show here that making siRNAs “gene-like,” via short complementary A
5–8
/T
5–8
3′ overhangs, increases complex stability, and hence RNase protection and gene silencing
in vitro
up to 10-fold. After decomplexation in the cytoplasm, sticky siRNA (ssiRNA) concatemers fall apart. ssiRNAs are therefore not inducing antiviral responses, as shown by the absence of IFN-β production. Finally, transfection experiments in the mouse lung show that ssiRNA should be particularly suited to silencing with linear polyethylenimine
in vivo
.
Modeling a layer 4-to-layer 2/3 module of a single column in rat neocortex: Interweaving
in vitro
and
in vivo
experimental observations
Authors: Sarid Leora , Bruno Randy , Sakmann Bert , Segev Idan , Feldmeyer Dirk
Published: October 2007

We report a step in constructing an
in silico
model of a neocortical column, focusing on the synaptic connection between layer 4 (L4) spiny neurons and L2/3 pyramidal cells in rat barrel cortex. It is based first on a detailed morphological and functional characterization of synaptically connected pairs of L4–L2/3 neurons from
in vitro
recordings and second, on
in vivo
recordings of voltage responses of L2/3 pyramidal cells to current pulses and to whisker deflection.
In vitro
data and a detailed compartmental model of L2/3 pyramidal cells enabled us to extract their specific membrane resistivity (≈16,000 ohms·cm
2
) and capacitance (≈0.8 μF/cm
2
) and the spatial distribution of L4–L2/3 synaptic contacts. The average peak conductance per L4 synaptic contact is 0.26 nS for the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid and 0.2 nS for NMDA receptors. The
in vivo
voltage response for current steps was then used to calibrate the model for
in vivo
conditions in the Down state. Consequently, the effect of a single whisker deflection was modeled by converging, on average, 350 ± 20 L4 axons onto the modeled L2/3 pyramidal cell. Based on values of synaptic conductance, the spatial distribution of L4 synapses on L2/3 dendrites, and the average
in vivo
spiking probability of L4 spiny neurons, the model predicts that the feed-forward L4-L2/3 connection on its own does not fire the L2/3 neuron. With a broader distribution in the number of L4 neurons or with slight synchrony among them, the L2/3 model does spike with low probability.
Microtubule-based nuclear movement occurs independently of centrosome positioning in migrating neurons
Authors: Umeshima Hiroki , Hirano Tomoo , Kengaku Mineko
Published: October 2007

During neuronal migration in the developing brain, it is thought that the centrosome precedes the nucleus and provides a cue for nuclear migration along the microtubules. In time-lapse imaging studies of radially migrating granule cells in mouse cerebellar slices, we observed that the movements of the nucleus and centrosome appeared to occur independently of each other. The nucleus often migrated ahead of the centrosome during its saltatory movement, negating the supposed role of the centrosome in pulling the nucleus. The nucleus was associated with dynamic microtubules enveloping the entire nucleus and stable microtubules extending from the leading process to the anterior part of the nucleus. Neither of these perinuclear microtubules converged at the centrosome. Disruption or excess formation of stable microtubules attenuated nuclear migration, indicating that the configuration of stable microtubules is crucial for nuclear migration. The inhibition of LIS1 function, a regulator of a microtubule motor dynein, specifically blocks nuclear migration without affecting the coupling of the centrosome and microtubules in the leading process, suggesting that movements of the nucleus and centrosome are differentially regulated by dynein motor function. Thus, the nucleus moves along the microtubules independently of the position of the centrosome in migrating neurons.
In the Name of Security
Authors: Moorehead Caroline
Published: October 2007

TORTURE HAS BEEN INSTITUTIONAL IN EGYPT FOR MANY YEARS. NOW THE IMAGES FROM ABU GHRAIB HAVE GIVEN IT A NEW LEGITIMACY THROUGHOUT THE ARAB WORLD
Rape as Torture?
Authors: Gunhammar Jessica
Published: October 2007

IMAGES OF ABU GHRAIB RECALL MEMORIES OF RAPE IN THE BALKANS
The Pain and the Memory: the Legacy of Nunca Más
Authors: Graham-Yooll Andrew
Published: October 2007

ALMOST A QUARTER-OF-A-CENTURY ON, ARGENTINA IS STILL GRAPPLING WITH THE MEMORY OF THE YEARS UNDER THE GENERALS
The Secrets of S21
Authors: Fawthrop Tom
Published: October 2007

CAMBODIA IS STILL WAITING FOR ITS CRIMINAL TRIBUNAL TO BRING TO JUSTICE THE PERPETRATORS OF POL POT’S GENOCIDE. MEANWHILE, THE TORTURERS WALK FREE, READY TO TELL THEIR TALE TO WHOEVER ASKS
Our Man in Uzbekistan
Authors: Murray Craig
Published: October 2007

Craig Murray, Britain’s former ambassador to Uzbekistan, has been portrayed in the media as a colourful and dotty rogue with a penchant for bars, girls, Range-Rovers and outrageous breaches of diplomatic protocol. In August 2003, he was confronted with a series of disciplinary charges by the Foreign Office, which he was not permitted to discuss with anyone, and instructed to resign. He refused and denied any allegations of wrongdoing. The allegations were reportedly dropped within weeks but not before Murray had had a breakdown and a pulmonary embolism that nearly killed him. He was finally removed from his post in October 2004. As an exercise in psychotherapy, he is now writing an autobiography so frank, he says, that it is unlikely ever to see the light of day: ‘mostly about sex and drinking’. Yet friends and supporters insist that he had his personal and professional life shredded for consistent, courageous criticism of US support for Uzbekistan’s ruthless and repressive regime, for highlighting its use of torture and bringing attention to the plight of its political and religious dissidents. IM
Return To the Great Game
Authors: Bensmann Marcus
Published: October 2007

AS RUSSIA AND THE USA JOCKEY FOR POWER, CENTRAL ASIA FINDS ITSELF ONCE MORE AT THE CENTRE OF A GREAT GAME
Dynasties and Dictators
Authors: Andersen Michael
Published: October 2007

THE SOVIET UNION BROKE UP 13 YEARS AGO, BUT THE COMMUNIST ELITES STAYED IN POWER: USING TRIED AND TRUSTED SOVIET METHODS THEY HAVE STOLEN WHOLE COUNTRIES AND ARE PREPARING TO HAND OVER THEIR CHILDREN’S INHERITANCE
A Suitable Case for Treatment
Authors: Ruzaliev Odil
Published: October 2007

THE ANNUAL AIDS EPIDEMIC UPDATE (UNAIDS DECEMBER 2004) CALLED UZBEKISTAN ‘THE YOUNGEST AIDS EPIDEMIC IN THE WORLD’. THE COUNTRY IS GEARING UP TO DEAL WITH THE PROBLEM, BUT SOCIAL ATTITUDES LAG FAR BEHIND
A Very Peaceful Jihad
Authors: Escobar Pablo
Published: October 2007

CENTRAL ASIA’S ISLAMISTS ARE NO TERRORISTS; ALL THEY WANT IS A MUSLIM UTOPIA WORLDWIDE AND PEACE AND PROSPERITY IN THE REGION. NOT QUITE HOW THE RULERS SEE IT
News, Views and the Internet
Authors: Kislov Danl , Kudriashov Andrei , Tait Arch
Published: October 2007

IF IT WEREN’T FOR THE INTERNET, NO ONE WOULD HAVE A CLUE WHAT’S REALLY GOING ON
Caenorhabditis elegans prom-1Is Required for Meiotic Prophase Progression and Homologous Chromosome Pairing
Authors: Jantsch Verena , Tang Lois , Pasierbek Pawel , Penkner Alexandra , Nayak Sudhir , Baudrimont Antoine , Schedl Tim , Gartner Anton , Loidl Josef
Published: October 2007

A novel gene, prom-1, was isolated in a screen for Caenorhabditis elegans mutants with increased apoptosis in the germline. prom-1 encodes an F-box protein with limited homology to the putative human tumor suppressor FBXO47. Mutations in the prom-1 locus cause a strong reduction in bivalent formation, which results in increased embryonic lethality and a Him phenotype. Furthermore, retarded and asynchronous nuclear reorganization as well as reduced homologous synapsis occur during meiotic prophase. Accumulation of recombination protein RAD-51 in meiotic nuclei suggests disturbed repair of double-stranded DNA breaks. Nuclei in prom-1 mutant gonads timely complete mitotic proliferation and premeiotic replication, but they undergo prolonged delay upon meiotic entry. We, therefore, propose that prom-1 regulates the timely progression through meiotic prophase I and that in its absence the recognition of homologous chromosomes is strongly impaired.
Synaptotagmin C2A Loop 2 Mediates Ca2+-dependent SNARE Interactions Essential for Ca2+-triggered Vesicle Exocytosis
Authors: Lynch K. L. , Gerona R.R.L. , Larsen E. C. , Marcia R. F. , Mitchell J. C. , Martin T.F.J.
Published: October 2007

Synaptotagmins contain tandem C2 domains and function as Ca2+ sensors for vesicle exocytosis but the mechanism for coupling Ca2+ rises to membrane fusion remains undefined. Synaptotagmins bind SNAREs, essential components of the membrane fusion machinery, but the role of these interactions in Ca2+-triggered vesicle exocytosis has not been directly assessed. We identified sites on synaptotagmin−1 that mediate Ca2+-dependent SNAP25 binding by zero-length cross-linking. Mutation of these sites in C2A and C2B eliminated Ca2+-dependent synaptotagmin−1 binding to SNAREs without affecting Ca2+-dependent membrane binding. The mutants failed to confer Ca2+ regulation on SNARE-dependent liposome fusion and failed to restore Ca2+-triggered vesicle exocytosis in synaptotagmin-deficient PC12 cells. The results provide direct evidence that Ca2+-dependent SNARE binding by synaptotagmin is essential for Ca2+-triggered vesicle exocytosis and that Ca2+-dependent membrane binding by itself is insufficient to trigger fusion. A structure-based model of the SNARE-binding surface of C2A provided a new view of how Ca2+-dependent SNARE and membrane binding occur simultaneously.
Identification of Novel Membrane-binding Domains in Multiple Yeast Cdc42 Effectors
Authors: Takahashi Satoe , Pryciak Peter M.
Published: October 2007

The Rho-type GTPase Cdc42 is a central regulator of eukaryotic cell polarity and signal transduction. In budding yeast, Cdc42 regulates polarity and mitogen-activated protein (MAP) kinase signaling in part through the PAK-family kinase Ste20. Activation of Ste20 requires a Cdc42/Rac interactive binding (CRIB) domain, which mediates its recruitment to membrane-associated Cdc42. Here, we identify a separate domain in Ste20 that interacts directly with membrane phospholipids and is critical for its function. This short region, termed the basic-rich (BR) domain, can target green fluorescent protein to the plasma membrane in vivo and binds PIP2-containing liposomes in vitro. Mutation of basic or hydrophobic residues in the BR domain abolishes polarized localization of Ste20 and its function in both MAP kinase–dependent and independent pathways. Thus, Cdc42 binding is required but is insufficient; instead, direct membrane binding by Ste20 is also required. Nevertheless, phospholipid specificity is not essential in vivo, because the BR domain can be replaced with several heterologous lipid-binding domains of varying lipid preferences. We also identify functionally important BR domains in two other yeast Cdc42 effectors, Gic1 and Gic2, suggesting that cooperation between protein–protein and protein–membrane interactions is a prevalent mechanism during Cdc42-regulated signaling and perhaps for other dynamic localization events at the cell cortex.
Dynamized Preparations in Cell Culture
Authors: Sunila Ellanzhiyil Surendran , Kuttan Ramadasan , Preethi Korengath Chandran , Kuttan Girija
Published: October 2007

Although reports on the efficacy of homeopathic medicines in animal models are limited, there are even fewer reports on the in vitro action of these dynamized preparations. We have evaluated the cytotoxic activity of 30C and 200C potencies of ten dynamized medicines against Dalton′s Lymphoma Ascites, Ehrlich′s Ascites Carcinoma, lung fibroblast (L929) and Chinese Hamster Ovary (CHO) cell lines and compared activity with their mother tinctures during short‐term and long‐term cell culture. The effect of dynamized medicines to induce apoptosis was also evaluated and we studied how dynamized medicines affected genes expressed during apoptosis. Mother tinctures as well as some dynamized medicines showed significant cytotoxicity to cells during short and long‐term incubation. Potentiated alcohol control did not produce any cytotoxicity at concentrations studied. The dynamized medicines were found to inhibit CHO cell colony formation and thymidine uptake in L929 cells and those of Thuja, Hydrastis and Carcinosinum were found to induce apoptosis in DLA cells. Moreover, dynamized Carcinosinum was found to induce the expression of p53 while dynamized Thuja produced characteristic laddering pattern in agarose gel electrophoresis of DNA. These results indicate that dynamized medicines possess cytotoxic as well as apoptosis‐inducing properties.
The Social Demand for a Medicine Focused on the Person: The Contribution of CAM to Healthcare and Healthgenesis
Authors: Roberti di Sarsina Paolo
Published: October 2007

The Non Conventional Medicines have a greater social impact and the demand for such treatments of more than 10 million Italian citizens (male and female) of all ages and social classes and of thousands of Italian families reveals an interest proving that there is a trend reversal, involving also other sectors of the medical and scientific world, which shifts the focus from the symptom to an idea of more general and comprehensive well‐being of the person. Over the last few years the scientific debate on Non Conventional Medicines and their integration with the academic or dominant medicine in our western society has favored and legitimated an increase in the demand and has activated a cultural transformation process involving the life styles. The focus is therefore shifted to the self‐healing capacities, to the reawakening of the individual potentialities, which support and amplify the benefits of the treatments and the citizens start pretending to be accurately informed in order to choose freely their own health program.
Herbal Medicines: Can We Do without Pharmacologist?
Authors: Calapai Gioacchino , Caputi Achille P.
Published: October 2007

The increase of herbal medicine use led many scientists to contribute to the research in this field. Also a few pharmacologists, after an initial phase of correct criticisms, today recognize the possibility of investigating the scientific value of medicinal products composed essentially of vegetable extracts. However, it is logical to pose the questions: (i) is there a role for the pharmacologist in herbal medicine (or phytotherapy)? (ii) can we do without pharmacologists’? First, two worlds—drug researchers (pharmacologists) and herbal medicines—yesterday appearing in opposition, are today closer and it is not unusual to read scientific works describing herbal extracts in journals traditionally dedicated to the study of synthetic drugs. Second, clinical application of herbal medicines is evaluable through the methods of modern clinical pharmacology. Efficacy and safety of medicinal plants represent naturally the object of interest for the pharmacologist and it is surely this aspect which gives the most important information on herbal medicine use. Many plants have been studied and results published showing, one time good or another poor, efficacy. Safety aspects of some of the most frequently used plants are now well known. For example, today we learn to use hypericum and we do not give it to patients taking other drugs because the interactions of hypericum with them. Contraindications of other plants, often represented by interactions with drugs, are finally known (Ginkgo biloba and drugs acting on blood coagulation). In conclusion, antagonistic behavior of pharmacologists versus herbal medicines is not useful. On the contrary, modern phytotherapy needs the contribution of researchers usually trained to evaluate efficacy and safety of medicinals.
Ear Acupuncture in European Traditional Medicine
Authors: Gori Luigi , Firenzuoli Fabio
Published: October 2007

Auricular acupuncture is a diagnostic and treatment system based on normalizing the body′s dysfunction through stimulation of definite points on the ear. Rudimentary forms of acupuncture which probably arose during the Stone Age have survived in many parts of the world right down to present day. It was used in the ancient Egypt, Rome, Greece and all the Mediterranean area. It is a microacupuncture technique similar to reflexology, and was first described in France in 1950 by Paul Nogier who is considered the Father of modern ear acupuncture. It was speculated that the technique works because groups of pluripotent cells contain information from the whole organism and create regional organization centers representing different parts of the body. Nevertheless stimulation of a reflex point in the ear seems relieve symptoms of distant pathologies. Modern research is confirming the efficacy of ear acupuncture for analgesia and anxiety related disease, while tobacco dependence and other substance abuse still need confirmation. Actually main methodological problems with auricular acupuncture are that exist too many maps with little agreement regarding point location in the ear, and that the correspondence or reflex systems does not correlated with modern knowledge of anatomy and physiology.
The Diseases of the Medici Family and the Use of Phytotherapy
Authors: Lippi Donatella
Published: October 2007

The Medici Project is a paleopathological and historico‐medical research, based on the exhumation of corpses of the Medici Family buried in the Medici Chapels (Florence, San Lorenzo). The scientific research carried out on these remains permits us to reconstruct habits and causes of death of members of this famous family of Italian Renaissance. The comparison between the literary sources and the paleopathological evidence is also important to reconstruct different therapies. Physicians, who assisted the most important persons of the Medici Family, have left a rich literature about their patients: the treatments were based on the use of plants and natural substances. Analyzing these sources is of unique importance and throws light on the therapeutical choices of the time.